Merge chore/graphify-recovery-doc into develop

The previous note said a fresh clone gets the skill back from `make
plugin` without naming the command, and I picked the wrong one when the
files actually went missing. There are two, and only one restores the
skill:

  - `graphify install --platform claude` copies SKILL.md, references/
    and .graphify_version. Touches nothing else. This is the recovery
    command, verified: the skill came back at 0.9.61 and the four
    guarded configs were byte-identical afterwards.
  - `graphify claude install` writes the CLAUDE.md section and the
    .claude/settings.json PreToolUse hooks, rewrites both of those
    guarded configs (EVAL-020, reproduced today), and does NOT copy the
    skill.

LRN-154 records why the files vanished in the first place. `git rm
--cached` keeps the working file, but `gitflow finish` checks out the
target branch, where it is still tracked, so git restores it and the
merge then deletes it from disk. .gitignore does not protect it; it only
stops a re-add. The file survives the commit and dies at the merge, which
reads as unrelated.

.claude/memory/decisions.md

@@ -97,6 +97,9 @@ rules:
 | BDR-085 | 2026-08-25 | User permanent rules: writing-style always-on in rules/, web build+security path-scoped | accepted |
 | BDR-086 | 2026-08-26 | darwin: threshold gates full loops; verified defects fixed regardless of unit score (paired-validated, batched checkpoint) | accepted |
 | BDR-087 | 2026-09-03 | Stop hook = attention signal only, never control flow; one script for Notification + Stop | accepted |
+| BDR-088 | 2026-09-15 | gstack Playwright bump shared via lib, re-applied after submodule update; update helper never touches the submodule tree | accepted |
+| BDR-089 | 2026-09-15 | No Playwright browser-cache pruner; read-only doctor report — .links proved 0 bytes reclaimable | accepted |
+| BDR-090 | 2026-09-15 | Destructive shell work → autoMode soft_deny/hard_deny; `ask` tier abandoned (inert under auto) | accepted |
 
 ---
 
@@ -1123,3 +1126,34 @@ Branch feature/user-writing-web-rules, UNMERGED (human gate).
 - **Guard vs prior refusal**: [[BDR-083]] (unlazy review, GATE 0) REFUSED a Stop hook using `decision:"block"` (forces continuation, inverts human gates). THIS Stop hook returns `terminalSequence` + `suppressOutput` only, exit 0, zero control-flow effect. Signal ≠ control. Do not read the refusal as banning Stop outright.
 - **Status**: accepted.
 - **Reference**: [[LRN-146]] event-coverage gap, [[BLK-020]] client-side faults, [[LRN-145]] terminalSequence pattern. Verified live: turn-end + AskUserQuestion both ring; `permission_prompt` unexercisable under `defaultMode: auto`.
+
+---
+
+## BDR-088 — gstack Playwright bump shared via lib; update helper never touches submodule tree
+- **Date**: 2026-09-15
+- **Decision**: `gstack_bump_playwright_if_unsupported` moved out of `install-plugins.sh` into `lib/gstack-playwright.sh`, sourced by install-plugins + update-all + doctor. update-all's submodule block now calls `gstack_submodule_update_with_bump`: re-applies bump after successful `submodule update --remote`; on failure prints git's own message, hints `make plugin`, returns 1. Never touches submodule worktree.
+- **Why**: [[BDR-029]] caveat open — bump survived only till next `make plugin`, update path never re-checked OS support. Real gap, user-reported.
+- **Alternatives rejected**: conflict-RECOVERY branch (discard package.json+bun.lock → retry → backup/restore). Withdrawn at human gate after 4-agent challenge: concentrated 3 BLOCKER + 4 MAJOR. Worst case = bump discarded, re-apply silently no-ops (bun absent / registry down — bump returns 0 on every path), `./setup` rebuilds browse against unsupported Playwright → [[BLK-008]] returns. Pre-existing behavior just failed the update and kept bump intact, so the "improvement" could regress a working install.
+- **Deviations carried from "code MOVED not changed"**: `|| true` on ostag capture (line exited 1 on every non-Ubuntu host → aborted caller under inherited errexit, reproduced); `timeout` on all 3 bun calls, exit 124 → warn + no bump (TERM'd install leaves node_modules half-written, poisons the support grep).
+- **Status**: accepted.
+- **Reference**: commit 2cebecb, `lib/gstack-playwright.sh`. Links [[BDR-029]], [[LRN-070]], [[LRN-071]], [[LRN-150]], [[BLK-008]].
+
+---
+
+## BDR-089 — No Playwright browser-cache pruner; read-only doctor report instead
+- **Date**: 2026-09-15
+- **Decision**: `doctor.sh` gains own `── Playwright browsers ──` section — cache size, per-revision the installs requiring it, counts of unreferenced dirs + broken links. Zero deletion anywhere in the lib.
+- **Why**: measured, not assumed. `~/.cache/ms-playwright/.links/` registers 3 installs — gstack 1.61.1 → rev 1228, gsd-pi nvm 1.61.0 → 1228, gsd-pi ~/.local 1.63.0 → 1243. Every dir on disk referenced → 0 bytes reclaimable. Playwright's own `_deleteStaleBrowsers` already unions across all registered installs on every `install`.
+- **Alternatives rejected**: hand-rolled pruner guarded on "revision resolved by gstack's local playwright" (the originally requested shape) — that guard keeps 1228 and DELETES 1243, breaking gsd-pi. The guard was wrong, not just its implementation.
+- **Status**: accepted.
+- **Reference**: commit 2cebecb. Links [[LRN-151]], [[BDR-088]].
+
+## BDR-090 — Destructive shell work → autoMode soft_deny/hard_deny; `ask` tier abandoned
+- **Date**: 2026-09-15
+- **Decision**: 10 rules leave the static tiers (user's own edit): `rsync` `kill -9` `killall` `pkill` out of `deny`; `python3 -c` `python -c` `xargs` `sed` `cp` `mv` out of `ask`. Cover rebuilt in `autoMode` — 7 `soft_deny` (write outside cwd, `rsync --delete`, SIGKILL/kill-by-name, in-place edit spanning >1 file, directory move, inline interpreter or `xargs` that deletes or writes outside cwd) + 3 `hard_deny` (secret exfiltration, prod deploy, disarming guardrails). Intent clears a soft block for the CURRENT TURN only — encoded as a rule line, no setting exists for it. `classifyAllShell` stays false. `permissions.deny` +10 `.env` reader rules (`sed awk cut tr sort uniq diff od xxd strings`), 6 of which sat in `allow`.
+- **Why**: `ask` raises no prompt under `defaultMode: auto` ([[LRN-146]], verified live). It gated nothing, so a destructive rule moved deny→ask was a silent loosening dressed as a confirmation. `soft_deny` = the tier the classifier enforces and user intent clears. `hard_deny` = the 3 classes no command pattern can express — read-then-send spans turns, a prod target is a name not a verb, widening a deny list is self-disarming.
+- **Alternatives rejected**: keep them in `ask` — inert, false sense of a gate. Back to `deny` — blocks legit process cleanup and inter-project copy, and the user works Bash-first under auto mode. `classifyAllShell: true` — closes the allow-tier blind spot but bills a classifier call on every `git status`. Published-history rewrite as `hard_deny` — user declined; `rebase` then an ordinary push stays uncovered, known gap.
+- **Scope fix (same commit)**: `autoMode.environment` named `/home/bchanot/Documents/atlast`, its FTP deploy target and its customer data, inside the file `link.sh:21` symlinks to `~/.claude/settings.json`. Every project received atlast's facts, and this repo's own Gitea remote contradicted the block's "no remote configured". Global block now machine-generic; atlast facts moved to atlast's gitignored `.claude/settings.local.json`.
+- **Caveat**: the guardrail `hard_deny` bars REMOVING a `deny`/`soft_deny`/`hard_deny` entry, not adding one. Future loosening goes through `/permissions` or the user's own edit — deliberate, confirmed with the user.
+- **Status**: accepted.
+- **Reference**: `settings.json`, `doctor.sh` `check_automode`, `templates/settings/SETTINGS.md`. Links [[LRN-153]], [[LRN-146]], [[BDR-004]].

.claude/memory/evals.md

@@ -39,6 +39,7 @@ rules:
 | EVAL-025 | 2026-07-17 | opening seo/geo inventory (subagents): 7/7 verifiable claims false or overstated; real contact corrected all, 6 plan corrections + 4 features killed at measurement | keep |
 | EVAL-027 | 2026-08-24 | contract-gates behavioral RED: 16/16 fresh unprimed runs followed new doctrine (GATE 0 order, vacuous oracle, ABANDONED routing, scope temptation resisted) | keep |
 | EVAL-028 | 2026-08-26 | darwin v2.1 paired run 54 units: 60 paired verdicts 0 revert/tie; skeptics found 3 real residuals — engaged, not rubber-stamp | keep |
+| EVAL-029 | 2026-09-15 | 4-agent plan challenge: 6 BLOCKER; 3 of 3 confirmation-pass BLOCKERs came from the fixes themselves; caught a false 654 MB orphan claim | keep |
 
 ---
 
@@ -267,3 +268,14 @@ Dogfood: 3 blind lenses attacked the v1 plan for the plan-challenge feature itse
 - **Method**: paired same-judge 3-majority per round (v2.1); judges live-exec where artifact executable (5 units: skills-perso, profile, plugin-pair, status-reporter, gitflow). Absolute scores triage-only. Totals main-thread (LRN-018 applied).
 - **Anomalies**: (1) 0 reverts/ties in 60 verdicts — homogeneous-better checked: skeptic lens found real residuals 3x (doctor.sh cost source, hotfix RULES leftover restore, FILE(S) new-marker) → judges engaged. (2) census lock RED on line-rewrap, make test caught → LRN-144. (3) head-pipe masked grep exit 2x → LRN-143.
 - **Action**: v2.1 paired = standard. Post-run absolute rescore skipped by design (would be judge-noise theater).
+
+---
+
+## EVAL-029 — 4-agent plan challenge: 6 BLOCKERs, and the fix round produced 3 of them
+- **Date**: 2026-09-15
+- **Method**: 3 blind lenses (correctness / robustness / simplicity) on plan rev 1, then 1 confirmation lens on rev 2. Subject = the gstack Playwright lib plan ([[BDR-088]]).
+- **Result**: rev 1 → 3 BLOCKER + 12 MAJOR. Rev 2, written specifically to close them → 3 NEW BLOCKERs, and 2 of the 3 were INTRODUCED BY the fixes: the new "every public function returns 0" rule contradicted the new "return rc", and the printer-name clause came verbatim from my own contract criterion 9. Rev 3 dropped the recovery branch entirely at the human gate — 6 findings closed by deletion instead of code.
+- **Anomaly**: my first user-facing answer asserted ~654 MB of orphan Playwright revisions. FALSE — `.links` showed every dir referenced, 0 reclaimable. Caught only while designing the guard, not while asserting the number. Worse, the guard I proposed would itself have deleted gsd-pi's rev 1243.
+- **Action**: (1) never state a disk-reclaimable figure before reading the registry that owns it ([[LRN-151]]). (2) A fix round deserves the same challenge as the original plan — 3/3 confirmation BLOCKERs came from fixes, not from the original. (3) The confirmation pass earned its cost: without it the printer override would have shipped and silently disconnected doctor's counters ([[LRN-150]]).
+- **Status**: keep.
+- **Reference**: `.claude/tasks/plans/2026-09-13-gstack-playwright-lib-2220.md` (rev 3). Links [[BDR-088]], [[LRN-150]].

.claude/memory/journal.md

@@ -460,3 +460,14 @@ rules:
 - Post-merge regression: toast dead again after re-attach from a RESTORED terminal, bell fine. Root cause [[LRN-147]]: ext hooks only terminals born after its activation; `enablePersistentSessions` restores terminals before it. Fix = disable persistent sessions, or fresh terminal + `dtach -a`. Verified: 3/3 toasts on fresh pty.
 - Same-day counter-example broke that cause: second session's terminal deaf though created LATER, same window, ext global, shells identical. Trigger unknown; [[LRN-148]] adds the 5s pre-flight test + demotes LRN-147's mechanism claim.
 - Attention signal refined: per-event labels (BDR-087 follow-on), silence on non-attention events, and no turn-end signal while `background_tasks` non-empty ([[LRN-149]]). Payload dump beat the docs: `background_tasks` undocumented for Stop but present on the wire. Branch bugfix/notify-subagent-spawn.
+- gstack Playwright: bump extracted to `lib/gstack-playwright.sh`, now re-applied after a successful submodule update ([[BDR-088]]); read-only browsers report in doctor, no pruner — `.links` proved 0 bytes reclaimable and the guard I first proposed would have deleted gsd-pi's rev 1243 ([[BDR-089]], [[LRN-151]]). 4 challengers → 6 BLOCKER, recovery branch withdrawn at the gate ([[EVAL-029]]). 2cebecb on feature/gstack-playwright-lib.
+- Node checked against Playwright: already v24 (1.61 needs >=18, 1.63 needs >=20), not the macOS constraint. macOS audit deferred to its own cycle — found statically: `sed -i` with no suffix x3 in install-plugins.sh (BSD sed eats the next arg), `${x,,}` in url-guard.sh (bash 4+, macOS ships 3.2), `readlink -f` in doctor.sh (absent pre-Monterey 12.3).
+
+## 2026-09-15
+- Aligned repo config + deployment on the user's hand-edited `settings.json`. Destructive shell work rebuilt in `autoMode` soft_deny/hard_deny once `ask` was established as inert under auto mode ([[BDR-090]]); `permissions.deny` +10 `.env` reader rules, 6 of which sat in `allow`.
+- `autoMode.environment` was scoped to ANOTHER project inside the user-scope file, so every repo got atlast's facts. Rewritten machine-generic, atlast facts moved to atlast's own `settings.local.json`, `$defaults` added to all three lists ([[LRN-153]]).
+- `doctor.sh` gained `check_automode` (missing `$defaults`, foreign-repo scope, both arms tested). `SETTINGS.md` documents the block + a tier-choice table. README's magic-MCP "ask = live confirmation" claim corrected — false under `defaultMode: auto`.
+- Found, not fixed: `.claude/settings.local.json` = 14.6 KB shadow copy of the global settings at HIGHER precedence, incl. a `config-protection.sh` hook whose script does not exist. Logged F1-F3 in TODO.
+- `make test` 0 RED, `doctor.sh` 0 errors, `shellcheck` clean.
+- graphify skill untracked + gitignored (written by `graphify install --platform claude` since `~/.claude/skills` symlinks to `skills/`). Cost one self-inflicted incident: `git rm --cached` kept the files, `gitflow finish` deleted them at the merge ([[LRN-154]]). Restored at 0.9.61, guarded configs snapshotted and verified untouched.
+- `.claude/settings.local.json` 14.6 KB -> 6.2 KB. It was not just duplication: its local `deny` still carried the 4 rules moved out of global deny, making [[BDR-090]]'s soft_deny a dead letter in this repo, and its `allow` carried `sed *` / `cp *` / `python3 -`, which short-circuit the classifier on the same rules.

.claude/memory/learnings.md

@@ -139,6 +139,11 @@ rules:
 | LRN-134 | 2026-07-17 | resolve-then-pin in stdlib http.client beats monkeypatching getaddrinfo — dual-stack, thread-safe, no requests; classify the OS-resolved IP not the URL text | closing SSRF/DNS-rebinding on any Python HTTP egress |
 | LRN-135 | 2026-07-17 | a prefix-only scan for a dangerous construct is bypassable by padding — scan the WHOLE document | refusing any hostile construct (DTD/directive/marker) before parse |
 | LRN-143 | 2026-08-26 | `cmd \| head \|\| fallback` — pipeline rc is head's (0), fallback dead; bounded output → drop head, else pipefail | any probe/fallback bash in skills before trusting `\|\|` |
+| LRN-150 | 2026-09-15 | Sourced lib shares caller shell: bare `ok/warn/info` override its printers, and its `set -e` applies inside | any new lib/*.sh |
+| LRN-151 | 2026-09-15 | Playwright cache truth = union over `.links`, dir name maps `_`→`-`, revisionOverrides exist | shared versioned binary caches |
+| LRN-152 | 2026-09-15 | git `protocol.file=user` blocks submodule fixtures; `-c` misses the code under test, `GIT_CONFIG_*` env does not | tests building git fixtures |
+| LRN-153 | 2026-09-15 | `autoMode` lists replace built-ins without `"$defaults"`; a user-scope block reaches every project | any `autoMode` edit |
+| LRN-154 | 2026-09-15 | `git rm --cached` + merge into a branch that still tracks the file DELETES it from disk | untracking a generated file |
 
 ---
 
@@ -1421,3 +1426,46 @@ Rule: when editing a doctrine file under structure locks, grep the test's lock s
 - **Fail-open**: field absent (older client) → still signal. Missed notification worse than extra one.
 - **Cross-session gotcha**: hook is user-scope, so EVERY session runs it. A single-file dump (`> file`) gets overwritten by another project's session — append JSONL and filter on `.cwd`. That accident proved `permission_prompt` fires with `message="Claude needs your permission"` (unexercisable in this session under `defaultMode: auto`).
 - **Future**: any hook needing turn-completion semantics must check background_tasks; "turn ended" ≠ "work done". Verified live: Stop with 0 tasks signals, Stop with 1 running subagent silent.
+
+---
+
+## LRN-150 — Sourced shell lib is not a subprocess: prefix printers, honor inherited errexit
+- **Date**: 2026-09-15
+- **Pattern**: `source lib.sh` shares the caller's shell. Two bites. (a) bare `ok()`/`warn()`/`info()` in the lib OVERRIDE the caller's same-named funcs. `doctor.sh` counts ERRORS/WARNS inside its own `warn()` → a lib `warn` disconnects the counter and doctor prints "No errors" while warnings scroll. Prefix every lib printer (`_gspw_ok`, `_gspw_warn`, `_gspw_info`). (b) caller's `set -euo pipefail` applies INSIDE the lib's functions: a failing command-substitution assignment (`x="$(. /etc/os-release; [ "$ID" = ubuntu ] && printf ...)"`) aborts the CALLER when the func is called as a bare statement. Reproduced — exit 1 on every non-Ubuntu host, latent in `install-plugins.sh` since [[BDR-029]].
+- **Rule**: public func called bare → `return 0` on every path + `|| true` on every capture. Func allowed to return non-zero → call it ONLY as an `if` condition.
+- **Future application**: any new `lib/*.sh` sourced by a script that owns printers or sets `-e`. Check BOTH facets before wiring; the printer one is silent (no error, just a lying summary).
+- **Reference**: `lib/gstack-playwright.sh`, `doctor.sh:12-15`. Links [[BDR-088]].
+
+---
+
+## LRN-151 — Playwright cache truth lives in `.links`, never in one install's view
+- **Date**: 2026-09-15
+- **Pattern**: `~/.cache/ms-playwright/.links/<sha1>` = one file per registered `playwright-core`, content = its path. Required set = UNION of `browsers.json` revisions across ALL of them. Dir name on disk = `${name//-/_}-${revision}`: `chromium-headless-shell` → `chromium_headless_shell-1228`. Miss that mapping and 2 live dirs read as orphan forever. `revisionOverrides` exists (webkit, ffmpeg on mac / debian11 / ubuntu20.04) so the base revision alone under-matches. Playwright prunes this set itself on every `install` (`_deleteStaleBrowsers`, coreBundle.js).
+- **Future application**: never call a browser dir orphan from one project's playwright view — read `.links` first. Generalizes to any tool with a shared versioned binary cache plus a registry of consumers: the consumer registry is the source of truth, not the consumer you happen to be standing in.
+- **Reference**: `lib/gstack-playwright.sh` `_gspw_browser_referenced`. Links [[BDR-089]], [[EVAL-029]].
+
+---
+
+## LRN-152 — git `protocol.file=user` kills submodule fixtures; `-c` misses the code under test
+- **Date**: 2026-09-15
+- **Pattern**: since the CVE-2022-39253 hardening git refuses submodule clone/fetch over a local path by default (git 2.53 → `protocol.file` = `user`). `-c protocol.file.allow=always` fixes the FIXTURE's own git calls but NOT the `git` the code under test spawns — fresh process, inherits nothing from `-c`. Export for the whole test process instead: `GIT_CONFIG_COUNT=1 GIT_CONFIG_KEY_0=protocol.file.allow GIT_CONFIG_VALUE_0=always`. Env propagates, `-c` does not.
+- **Also**: fixture repos need LOCAL `user.email`/`user.name` (no global identity here) and `git init -b main` + explicit `submodule.<name>.branch`, else `--remote` resolves a different branch than production does.
+- **Future application**: any test building a git submodule fixture. Symptom is a hard "transport 'file' not allowed" before the first assertion, which reads like a broken test rather than a policy.
+- **Reference**: `lib/tests/gstack-playwright.test.sh`.
+
+## LRN-153 — `autoMode` lists replace built-ins unless `"$defaults"` is spliced in
+- **Date**: 2026-09-15
+- **Pattern**: every list under `autoMode` (`allow` `soft_deny` `hard_deny` `environment`) is a FULL replacement by default. Omit the literal `"$defaults"` and the built-in classifier rules are dropped silently — no warning, no schema error, the classifier just runs thinner. Put `"$defaults"` first, own entries after: built-ins inherited, then refined.
+- **Scope trap, same block**: `autoMode` in `~/.claude/settings.json` reaches EVERY project. A block generated while working in one repo (its deploy target, its secrets, its data) ships that repo's facts to all the others, and contradicts whichever repo is actually open. Project facts belong in that project's `.claude/settings.local.json`.
+- **Format**: these lists are prose spliced into the classifier prompt, not permission-rule syntax. Write "Sending SIGKILL reaches processes outside this session", never `Bash(kill -9 *)`.
+- **Backstop**: `doctor.sh` `check_automode` warns on a list missing `$defaults` and on a user-scope `environment` naming a git repo other than the config repo. Both arms exercised against the defective block before shipping.
+- **Future application**: any `autoMode` edit — check `$defaults` presence and scope before anything else.
+- **Reference**: `doctor.sh`, `templates/settings/SETTINGS.md`. Links [[BDR-090]].
+
+## LRN-154 — Untracking a generated file then merging deletes it from disk
+- **Date**: 2026-09-15
+- **Pattern**: `git rm --cached` removes from the index and KEEPS the working file, which is the whole point when untracking a tool-generated artifact. But `gitflow finish` checks out the target branch first, where the file is still tracked, so git restores it; the merge then applies the deletion to a tracked file and removes it from disk. `.gitignore` does not protect it — it only stops a re-add. Net effect: the file survives the commit and dies at the merge, several minutes later, which reads as unrelated.
+- **Detection**: the working tree is clean and the file is simply absent. Nothing errors. Only a post-merge `ls` catches it.
+- **Future application**: untracking any generated file — know the regeneration command BEFORE merging, and `ls` the path right after `finish`. If nothing regenerates it, keep it tracked.
+- **graphify specifics**: `graphify install --platform claude` copies the skill and touches nothing else. `graphify claude install` is a different command — it writes the CLAUDE.md section and the `.claude/settings.json` hooks, rewrites both guarded configs, and does NOT copy the skill. Confusing the two wastes a recovery attempt.
+- **Reference**: `CLAUDE.md` machine-owned section, commit 80ccdaf. Links [[BDR-090]].

.claude/tasks/TODO.md

@@ -1,5 +1,110 @@
 # TODO
 
+## 2026-09-15 — align config + deployment on the hand-edited settings.json (feature/automode-config-alignment)
+User edited global `settings.json` by hand: 4 destructive rules moved
+deny→ask (`rsync`, `kill -9`, `killall`, `pkill`), 4 removed from ask
+(`xargs`, `sed`, `cp`, `mv` — coherent with auto mode's Bash-first
+workflow; the `.env`-scoped `cp`/`mv`/`xargs` deny rules still stand),
+and an `autoMode.environment` block added. Two defects found:
+(1) the environment block describes **atlast** (`bin/deploy.sh` lftp/FTP
+to OVH, quote-request data, "no remote configured") but lives in the
+user-scope file symlinked to `~/.claude/settings.json` by `link.sh:21`
+— so every project gets atlast's facts; claude-config itself has a
+Gitea remote, contradicting the block. (2) no `"$defaults"` sentinel,
+so the built-in classifier environment entries are replaced, not
+extended. Third finding: LRN-146 records, verified in session, that
+`ask` rules raise no prompt under `defaultMode: auto` — the deny→ask
+move therefore traded a static block for a classifier decision.
+User decisions (2026-09-15): atlast block → atlast's own
+`settings.local.json`, global block rewritten machine-generic; the 4
+destructive rules → `autoMode.soft_deny` (the section that actually
+binds under auto mode) instead of `ask`.
+- [x] T1 global `settings.json` — machine-generic `autoMode.environment`
+      with `$defaults`; new `autoMode.soft_deny` with `$defaults` + the
+      4 destructive rules; drop those 4 from `permissions.ask`
+- [x] T2 `/home/bchanot/Documents/atlast/.claude/settings.local.json` —
+      receives the atlast-specific `autoMode.environment` (gitignored,
+      personal scope); verify project-scope `autoMode` is honored
+- [x] T3 `templates/settings/SETTINGS.md` — document the `autoMode`
+      block (environment / soft_deny / hard_deny / allow, `$defaults`
+      semantics, `classifyAllShell`) + the "ask ≠ prompt under auto"
+      caveat that makes soft_deny the right tier
+- [x] T4 `README.md` — magic-MCP paragraph claims the `ask` tier makes
+      every `mcp__magic__*` call "require a live confirmation and never
+      auto-execute"; false under auto mode per LRN-146. Correct the
+      claim, flag the soft_deny option to the user (don't decide it)
+- [x] T5 `doctor.sh` — permissions section is blind to `autoMode`, now a
+      live security surface. Add a check: block present, `$defaults`
+      inherited, no foreign absolute project path hardcoded
+- [x] T6a CHANGELOG (Added/Changed/Fixed under [Unreleased])
+- [ ] T6b registries BDR-090 + LRN-153 + journal — drafted, awaiting user approval
+- [x] T7 verify: `make test`, `bash doctor.sh`, `shellcheck`
+NOT in scope: the 3 dirty `skills/graphify/*` files (pre-existing,
+unrelated) — never staged.
+
+### Second pass (2026-09-15, user decisions)
+User confirmed the `ask` removals were deliberate (`/permissions`), asked
+for the diff vs develop and for guards where the removals left a hole.
+Answered: writes outside cwd → soft_deny; in-place edits beyond one named
+file → soft_deny; inline interpreters + `xargs` → soft_deny when they
+delete or write outside cwd; hard_deny for secret exfiltration, prod
+deploy, disarming guardrails (history rewrite NOT retained, so a `rebase`
+then an ordinary push stays uncovered); extend the static deny family to
+the `.env` readers; `classifyAllShell` stays false; intent clears a soft
+block for the CURRENT TURN only.
+- [x] S1 `permissions.deny` +10 reader rules (sed awk cut tr sort uniq
+      diff od xxd strings vs `.env*`) — 6 of them were in `allow`
+- [x] S2 `autoMode.soft_deny` — 7 rules + the intent-scope line
+- [x] S3 `autoMode.hard_deny` — 3 rules, "adding a restriction is fine,
+      removing one is not"
+- [x] S4 `SETTINGS.md` — tier-choice table + scope-of-intent section
+- [x] S5 CHANGELOG — Changed rewritten, new Security block
+- [x] S6 CONSEQUENCE confirmed by user 2026-09-15: the hard_deny guardrail rule means I can
+      no longer edit a deny/soft_deny/hard_deny list to REMOVE an entry.
+      Tightening stays allowed. Future permission loosening goes through
+      `/permissions` or the user's own edit.
+
+### Third pass (2026-09-15) — F1-F3 done + graphify untracked
+Worst finding was not the duplication: local `deny` still carried
+`rsync` `kill -9` `killall` `pkill`, the four the user moved OUT of
+global deny. deny wins across sources, so `autoMode.soft_deny` was a
+dead letter in THIS repo. Local `allow` also held `sed *`, `cp *`,
+`python3 -` — an allow rule short-circuits the classifier, punching a
+hole through the same soft_deny rules.
+- [x] G1 `skills/graphify/{SKILL.md,references/,.graphify_version}`
+      gitignored + `git rm --cached`. Written by `graphify claude
+      install` since `~/.claude/skills` symlinks to `skills/`; a fresh
+      clone gets them from `make plugin`. `test-prompts.json` is
+      hand-written for darwin, stays tracked. Trade-off documented in
+      CLAUDE.md: an upstream release can now change the skill prompt
+      with no diff to review.
+- [x] G2 `.claude/settings.local.json` 14.6 KB -> 6.2 KB. deny + ask
+      dropped whole, allow 185 -> 98 (81 duplicates of the global, 6
+      policy conflicts: `sed *`, `cp *`, `python3 -`,
+      `Read(//home/bchanot/**)`, `WebSearch`, a leftover injection-test
+      payload). Every non-`permissions` key was a verbatim copy of the
+      global, `hooks` included. Backup: `.audit/settings.local.json.bak-*`
+      (gitignored, the file itself is not in git).
+
+### Follow-up found while doing this (fixed in the third pass above)
+`.claude/settings.local.json` (gitignored, 14.6 KB) is a near-complete
+shadow copy of the global `settings.json` at a HIGHER precedence tier:
+185 allow / 30 ask / 106 deny, plus its own `cleanupPeriodDays`,
+`attribution`, `statusLine`, `enabledPlugins`, `extraKnownMarketplaces`,
+`effortLevel`, `remoteControlAtStartup`, `inputNeededNotifEnabled`,
+`skipAutoPermissionPrompt` — all identical to the global today, so the
+duplication is invisible until the global drifts, which it just did
+(no `autoMode`, 106 deny vs 116). It defeats the config-guard premise
+(hand-curated `settings.json`) with a file nobody reviews.
+- [x] F1 `WebSearch` sits in global `ask` and in local `allow` — in this
+      repo it never reaches the ask tier. Intended or drift?
+- [x] F2 local `hooks` block registers `bash ~/.claude/hooks/config-protection.sh`
+      on PreToolUse/Bash. That script does not exist, in `hooks/` or in
+      `~/.claude/hooks/`. Dead hook firing on every Bash call here.
+- [x] F3 decide: prune the local file down to the session-accumulated
+      allow rules only, dropping every key that merely restates the
+      global, or keep the copy deliberately and document why.
+
 ## 2026-08-25 — darwin fresh baseline: 32 skill-systems + 23 agents (feature/darwin-optimize-20260825)
 User: `/darwin-skill all skills and agents` (background). Fresh-from-zero
 (results.tsv wiped 2026-06-23, journal 2026-06-30). Scope per BDR-015/043 +

.claude/tasks/contracts/2026-09-13-gstack-playwright-lib-2220.md

@@ -0,0 +1,115 @@
+# CONTRACT — gstack-playwright-lib
+- date: 2026-09-13 | flow: feat | branch: feature/gstack-playwright-lib
+- status: active
+
+## REQUEST (verbatim — IMMUTABLE)
+
+Message 1:
+> l'installation de chromium, c'est une version fix ou en latest ? Il faudrait mettre en lateste, et d'ailleurs son update est pris en compt dans l'update ? quelq version a besoin gstack ? Ca serait pas plus simple d'installer perplexity a la place ?
+
+Message 2 (after the assistant proposed fix A + fix B):
+> les deux
+
+Message 3 (answer to the scope question on fix B, after the "654 Mo orphelins"
+premise was proven wrong):
+> Check read-only dans doctor.sh
+
+## CLARIFICATIONS
+
+Q: "mettre en latest" — pin Chromium to latest?
+A: Not actionable as asked. Playwright downloads the browser revision its own
+   version pins (1.61.1 → chromium 1228); the CDP client is coupled to that
+   build. "Latest" = track the latest Playwright, which is what BDR-029's bump
+   already does. No change to the pinning mechanism is in scope.
+
+Q: Volet B — purge the orphan Playwright revisions?
+A: Superseded by evidence. `~/.cache/ms-playwright/.links/` registers THREE
+   playwright installs (gstack 1.61.1 → rev 1228; gsd-pi nvm 1.61.0 → 1228;
+   gsd-pi ~/.local 1.63.0 → 1243). Every directory on disk is referenced;
+   zero bytes reclaimable. Playwright already GCs correctly on every
+   `install` (`_deleteStaleBrowsers`, unions across all registered installs).
+   User chose: read-only report in doctor.sh, NO deletion anywhere.
+
+## ACCEPTANCE CRITERIA
+
+1. `lib/gstack-playwright.sh` exists, is source-safe (sourcing prints nothing
+   and runs no side effect), and its verb dispatcher works when executed.
+   CHECK: out=$( . lib/gstack-playwright.sh; echo READY ); [ "$out" = READY ] && bash lib/gstack-playwright.sh 2>&1 | grep -q 'usage:' && echo LIB_OK
+   EXPECT: LIB_OK
+   EVIDENCE: MET exit=0 marker-found :: LIB_OK
+
+2. The bump logic lives ONLY in the lib: `install-plugins.sh` no longer
+   defines `gstack_bump_playwright_if_unsupported`, sources the lib instead,
+   and still calls it BEFORE gstack `./setup` (BDR-029 behavior unchanged:
+   OS-gated, idempotent, non-fatal).
+   CHECK: grep -q '^gstack_bump_playwright_if_unsupported() {' install-plugins.sh && exit 1; grep -q 'lib/gstack-playwright.sh' install-plugins.sh || exit 1; c=$(grep -n 'gstack_bump_playwright_if_unsupported' install-plugins.sh | grep -v ':[[:space:]]*#' | tail -1 | cut -d: -f1); s=$(grep -n '&& \./setup)' install-plugins.sh | head -1 | cut -d: -f1); [ -n "$c" ] && [ -n "$s" ] && [ "$c" -lt "$s" ] && echo EXTRACT_OK
+   EXPECT: EXTRACT_OK
+   EVIDENCE: MET exit=0 marker-found :: EXTRACT_OK
+
+3. `update-all.sh` delegates the gstack submodule update to the lib
+   (`gstack_submodule_update_with_bump`) instead of calling
+   `git submodule update --remote` bare, so the bump is re-applied after every
+   successful update.
+   CHECK: grep -q 'gstack_submodule_update_with_bump' update-all.sh && grep -q 'lib/gstack-playwright.sh' update-all.sh && ! grep -qE '^[[:space:]]*if git submodule update --remote skills-external/gstack' update-all.sh && echo WIRED_OK
+   EXPECT: WIRED_OK
+   EVIDENCE: MET exit=0 marker-found :: WIRED_OK
+
+4. [gated 2026-09-15] `gstack_submodule_update_with_bump` NEVER modifies the
+   submodule working tree. On a successful `git submodule update --remote` it
+   re-applies the bump; on failure it returns non-zero, touches nothing, and
+   emits git's own message plus a hint naming the local Playwright bump when
+   `package.json`/`bun.lock` are the dirty files. The conflict-RECOVERY branch
+   of the earlier revision (discard, retry, backup, restore) is withdrawn: it
+   could leave the bump discarded and un-reapplied, regressing a working
+   browser into BLK-008, which the pre-existing behavior never did.
+   CHECK: sed 's/#.*//' lib/gstack-playwright.sh | grep -qE 'git [^|;]*(checkout|reset|clean|stash)' && exit 1; bash lib/tests/gstack-playwright.test.sh 2>&1 | grep -q 'update-conflict' && bash lib/tests/gstack-playwright.test.sh 2>&1 | grep -qE '^PASS=[0-9]+ FAIL=0$' && echo NONDESTRUCTIVE_OK
+   EXPECT: NONDESTRUCTIVE_OK
+   EVIDENCE: MET exit=0 marker-found :: NONDESTRUCTIVE_OK
+
+5. `doctor.sh` prints a Playwright-browsers section: total cache size, one line
+   per browser directory naming the registered playwright install(s) that
+   reference it, plus counts of unreferenced directories and broken links.
+   CHECK: bash doctor.sh 2>/dev/null | grep -qi 'playwright browsers' && bash lib/gstack-playwright.sh browsers-report | grep -qE 'chromium-[0-9]+' && bash lib/gstack-playwright.sh browsers-report | grep -qi 'unreferenced' && echo REPORT_OK
+   EXPECT: REPORT_OK
+   EVIDENCE: MET exit=0 marker-found :: REPORT_OK
+
+6. The report is provably read-only: no destructive verb anywhere in the lib,
+   and the cache directory listing is identical before and after a report run.
+   CHECK: sed 's/#.*//' lib/gstack-playwright.sh | grep -qwE '(rm|rmdir|unlink|truncate|mv)' && exit 1; b=$(ls -la ~/.cache/ms-playwright ~/.cache/ms-playwright/.links 2>/dev/null | cksum); bash lib/gstack-playwright.sh browsers-report >/dev/null 2>&1; a=$(ls -la ~/.cache/ms-playwright ~/.cache/ms-playwright/.links 2>/dev/null | cksum); [ "$b" = "$a" ] && echo READONLY_OK
+   EXPECT: READONLY_OK
+   EVIDENCE: MET exit=0 marker-found :: READONLY_OK
+
+7. `lib/tests/gstack-playwright.test.sh` exists, passes, and covers at least:
+   bump skipped when the OS tag is already supported; bump fired when it is
+   not; submodule-update conflict recovery; browsers-report on a fixture cache
+   holding a referenced revision, an unreferenced one and a broken link.
+   CHECK: bash lib/tests/gstack-playwright.test.sh | tail -1 | grep -qE '^PASS=[0-9]+ FAIL=0$' && echo TESTS_OK
+   EXPECT: TESTS_OK
+   EVIDENCE: MET exit=0 marker-found :: TESTS_OK
+
+8. shellcheck clean on every touched shell file.
+   CHECK: shellcheck lib/gstack-playwright.sh lib/tests/gstack-playwright.test.sh install-plugins.sh update-all.sh doctor.sh >/dev/null 2>&1 && echo SHELLCHECK_OK
+   EXPECT: SHELLCHECK_OK
+   EVIDENCE: MET exit=0 marker-found :: SHELLCHECK_OK
+
+9. [gated 2026-09-15] (judgement) No new dependency; the report degrades
+   silently when `~/.cache/ms-playwright` is absent, when its `.links`
+   directory is absent, when `PLAYWRIGHT_BROWSERS_PATH` is `0` or not a
+   directory, or when no playwright install is registered — doctor must stay
+   green on a machine that never installed a browser. The lib's printers are
+   named `_gspw_ok`/`_gspw_warn`/`_gspw_info` and it defines NO bare
+   `ok`/`warn`/`info`/`pass`/`fail`: doctor.sh sources the lib before every
+   check, so bare names would override its own printers and silently
+   disconnect its `ERRORS`/`WARNS` counters.
+
+## FILE SCOPE
+
+- lib/gstack-playwright.sh            (new)
+- lib/tests/gstack-playwright.test.sh (new)
+- install-plugins.sh                  (remove inline fn, source + call lib)
+- update-all.sh                       (call bump + conflict recovery)
+- doctor.sh                           (new read-only report section)
+
+Out of scope: the gstack submodule itself, the pinning mechanism, any
+deletion of cached browsers, the `GSTACK_CHROMIUM_NO_SANDBOX` layer
+(LRN-040 layer 2, unchanged).

.claude/tasks/plans/2026-09-13-gstack-playwright-lib-2220.md

@@ -0,0 +1,201 @@
+# PLAN — gstack-playwright-lib (feat) — REVISION 3
+
+Contract: `.claude/tasks/contracts/2026-09-13-gstack-playwright-lib-2220.md`
+Revision 3 (2026-09-15). Rev 1 → 3-lens challenge → rev 2 → confirmation pass
+→ rev 3. The conflict-RECOVERY branch is WITHDRAWN at the human gate: it
+concentrated 3 BLOCKERs and 4 MAJORs, and its worst case regressed a working
+browser into BLK-008, which the pre-existing behavior never did.
+
+## Context
+
+- Chromium is not an apt package. It is the browser revision pinned by the
+  installed Playwright (`gstack/setup:483`). gstack: playwright 1.61.1 →
+  chromium rev 1228 (`Chrome for Testing 149`).
+- `~/.cache/ms-playwright/.links/` registers 3 playwright installs: gstack
+  1.61.1 (1228), gsd-pi nvm 1.61.0 (1228), gsd-pi ~/.local 1.63.0 (1243).
+  Every dir on disk is referenced → 0 bytes reclaimable. Playwright already
+  prunes correctly on every `install` (`_deleteStaleBrowsers`). No pruner is
+  written here.
+- The gstack submodule is intentionally dirty: `package.json` + `bun.lock`
+  carry the BDR-029 bump; `.gitmodules` sets `ignore = dirty`. It also carries
+  an untracked `?? bin/bin`.
+- `update-all.sh:87` calls `git submodule update --remote` bare, swallows
+  stderr, and never re-applies the bump afterwards. THAT is the gap.
+
+## Hard constraints the code must respect
+
+**Inherited errexit.** All three callers run `set -euo pipefail` and source
+the lib. `gstack_bump_playwright_if_unsupported` and `gstack_browsers_report`
+are called as bare statements, so they MUST `return 0` on every path and every
+capture inside them takes `|| true`.
+`gstack_submodule_update_with_bump` is the ONE exception: it returns non-zero
+on failure and is therefore called ONLY as an `if` condition, keeping
+`update-all.sh:87`'s existing `if / else warn` shape. An offline update stays
+non-fatal, exactly as today.
+
+**Printer names.** The lib defines `_gspw_ok`, `_gspw_warn`, `_gspw_info` and
+NEVER a bare `ok`/`warn`/`info`/`pass`/`fail`. `doctor.sh:22` sources the lib
+before every check, so bare names would override `doctor.sh:12-15` and
+silently disconnect its `ERRORS`/`WARNS` counters.
+
+**No destructive command in the lib, at all.** No `rm`, `rmdir`, `unlink`,
+`truncate`, `mv`, and no `git checkout`/`reset`/`clean`/`stash`. Contract
+criteria 4 and 6 both grep for this.
+
+**macOS-safe.** No `timeout` without a `command -v` guard (absent from stock
+macOS), no `readlink -f` (absent before Monterey 12.3), no `md5sum`, no
+`sed -i` without a suffix, no bash-4-only expansions (`${x,,}`), no `grep -P`.
+
+## Files
+
+1. `lib/gstack-playwright.sh` — NEW. Sourceable lib + verb dispatcher. No
+   `set -euo pipefail` at top level (mirrors `lib/detect-plugins.sh`).
+   Dispatcher guarded by `[ "${BASH_SOURCE[0]}" = "${0}" ]`, exposing
+   `browsers-report` ONLY. Any other argument → `usage:` on stderr, exit 2.
+   The write functions stay sourced-only: a CLI verb would expose
+   `bun add playwright@latest` as a command-line entry point.
+
+   - `_gspw_ok` / `_gspw_warn` / `_gspw_info <msg>` — fixed-prefix printers.
+   - `gstack_pw_ostag [os_release_path]` — prints `ubuntu<VERSION_ID>` for
+     Ubuntu, nothing otherwise. The capture takes `|| true`: the moved line
+     exits 1 on every non-Ubuntu host and would abort the caller under
+     inherited errexit. `return 0` always.
+   - `gstack_pw_supports <playwright_core_lib_dir> <ostag>` — 0/1 by grep.
+   - `gstack_bump_playwright_if_unsupported <gstack_dir>` — BDR-029 logic,
+     parameterized. Prepends `$HOME/.bun/bin` to PATH when `bun` is not
+     resolvable (LRN-036). Wraps ALL THREE bun invocations
+     (`bun install --frozen-lockfile`, the `bun install` fallback,
+     `bun add playwright@latest`) in `timeout 300` when `command -v timeout`
+     succeeds, plain otherwise. Exit 124 from any of them → `_gspw_warn` and
+     `return 0` WITHOUT attempting the bump: a TERM'd install leaves
+     `node_modules` half-written, and the support grep would then read a
+     truncated tree. One `_gspw_info` line before the network work so a
+     stalled registry is visible. `return 0` on every path (BDR-029
+     non-fatal).
+   - `gstack_submodule_update_with_bump <repo> [sub_path]`:
+     1. `git -C "$repo" submodule update --remote "$sub"`, stderr captured.
+     2. exit 0 → `gstack_bump_playwright_if_unsupported "$repo/$sub"` →
+        `return 0`.
+     3. exit != 0 → `_gspw_warn` with git's own message, verbatim and
+        unparsed. Then, when `git -C "$sub" status --porcelain --
+        package.json bun.lock` is non-empty, one extra `_gspw_info` hint line
+        naming the local Playwright bump and pointing at `make plugin`.
+        `return 1`. NOTHING in the working tree is touched.
+     No locale pin is needed: git's message is displayed, never parsed for a
+     decision. The hint is advisory, so its constant-true condition is
+     correct here, unlike the withdrawn recovery branch where it gated a
+     destructive step.
+   - `_gspw_browser_referenced <playwright_core_path> <dir_name>` — does that
+     install require this cache directory? Splits `<dir_name>` into name +
+     revision on the LAST `-`, then normalizes `_` → `-` on the name
+     (Playwright writes `chromium_headless_shell-1228` while `browsers.json`
+     says `chromium-headless-shell`; without this, two live directories are
+     reported unreferenced forever). Matches the base `revision` OR any value
+     under that browser's `revisionOverrides` (webkit and ffmpeg carry them
+     for mac and debian11 and ubuntu20.04 hosts). awk only: no jq, no
+     python3, no fallback ladder.
+   - `_gspw_install_label <playwright_core_path>` — `<dir-before-node_modules>
+     <version>`, e.g. `gstack 1.61.1`, `gsd-pi 1.63.0`.
+   - `gstack_browsers_report [cache_dir]` — read-only. Resolves the cache as
+     `${1:-${PLAYWRIGHT_BROWSERS_PATH:-$HOME/.cache/ms-playwright}}`; the
+     documented value `0` means "bundle into node_modules", so `0` and any
+     non-directory degrade to the silent no-cache path. Prints the header
+     `Playwright browsers`, the total from `du -sh … || true`, one line per
+     cache dir matching `*-<digits>` with the installs requiring it, then
+     `<N> unreferenced, <M> broken link(s)`. When N or M > 0, one
+     `_gspw_warn` naming them and the remedy, phrased without the words `rm`
+     or `mv` (criterion 6 word-greps the source): "re-run `playwright
+     install`, which prunes stale revisions". A dir whose NAME is listed by
+     some install but at another revision counts as `unknown revision`, not
+     unreferenced. `return 0` on every path.
+
+2. `install-plugins.sh` — delete the inline function (294-321), source the lib
+   next to detect-plugins (line 30), call site at ~370 becomes
+   `gstack_bump_playwright_if_unsupported "$GSTACK_DIR"`.
+
+3. `update-all.sh` — source the lib next to detect-plugins (line 19). Line 87
+   becomes `if gstack_submodule_update_with_bump "$REPO"; then` and the
+   existing `else warn …` arm is KEPT verbatim. No other structural change.
+
+4. `doctor.sh` — source the lib next to detect-plugins (line 22). Add its own
+   `── Playwright browsers ──` section (NOT nested under gstack: 2 of the 3
+   registered installs are gsd-pi), called as `gstack_browsers_report || true`.
+
+5. `lib/tests/gstack-playwright.test.sh` — NEW, auto-globbed by `make test`.
+
+## Edge cases
+
+- Every public function except the update returns 0 under the callers'
+  `set -euo pipefail`, including the all-zero-counts case, which is this
+  machine's nominal state and would otherwise kill `doctor.sh` before its
+  summary and take `update-all.sh:519` down with it.
+- `.links` entry whose target is gone or whose `browsers.json` is unreadable
+  → counted as a broken link, never dereferenced further.
+- Two installs of the same tool at different versions → both labels listed.
+- gstack submodule absent → bump and update both no-op 0.
+- Sourcing the lib prints nothing and does not change the caller's options.
+
+## Tests (`lib/tests/gstack-playwright.test.sh`)
+
+Shape of `lib/tests/fast-libs.test.sh` (`check` helper, `PASS=n FAIL=n` last
+line, `mktemp -d` + trap). git 2.53 defaults `protocol.file` to `user`, which
+blocks submodule clone and fetch. The fixture git calls are not enough: the
+`git submodule update --remote` under test runs INSIDE the lib, in a fresh
+process. So the test exports, for the whole test process,
+`GIT_CONFIG_COUNT=1 GIT_CONFIG_KEY_0=protocol.file.allow
+GIT_CONFIG_VALUE_0=always`, which the lib's own git inherits. Fixtures use
+`git init -b main` with `submodule.<name>.branch = main` set explicitly, so
+`--remote` resolves the way production does.
+
+- `T1-ostag-ubuntu` / `T2-ostag-other`: fixture os-release files.
+- `T3-errexit-safe`: the bump called as a bare statement under
+  `set -euo pipefail` with a non-Ubuntu os-release → the script reaches the
+  next line. Regression test for the latent abort.
+- `T4-supports-hit` / `T5-supports-miss`: fixture lib dir with and without the
+  tag. Proves idempotence both ways without invoking bun.
+- `T6-update-success-bumps`: fixture superproject + submodule, an upstream
+  commit, bump stubbed by redefining it after sourcing → update succeeds, the
+  stub ran once, returns 0.
+- `T7-update-conflict-nondestructive`: local edit to the submodule's
+  `package.json` plus a conflicting upstream commit → returns non-zero, BOTH
+  bump-owned files are byte-identical to before the call, and the hint line
+  was printed. Carries the literal `update-conflict` (contract criterion 4).
+- `T8-no-destructive-command`: greps the lib source for `git
+  checkout|reset|clean|stash` and for `rm|rmdir|unlink|truncate|mv` outside
+  comments. Stronger than criterion 6 alone.
+- `T9-report-referenced`, `T10-report-underscore-dir`
+  (`chromium_headless_shell-1228` against a `chromium-headless-shell` entry),
+  `T11-report-unreferenced`, `T12-report-broken-link`,
+  `T13-report-revision-override`: fixture cache + `.links` → fixture
+  playwright-core dirs with hand-written `browsers.json`.
+- `T14-report-zero-counts-exit-0`: everything referenced → exit 0. The nominal
+  case, not covered by the absent-dir case.
+- `T15-report-no-cache` / `T16-report-browsers-path-zero`: exit 0, nothing on
+  stderr.
+- `T17-source-safe`: sourcing emits nothing.
+
+## Disposition (STEP 0.6)
+
+- honors **BDR-029** by keeping the bump OS-gated, idempotent, non-fatal, and
+  by closing its stated caveat: the bump is now re-applied after every
+  successful update, not only at the next `make plugin`.
+- honors **LRN-024** by extracting a helper and refactoring the existing
+  caller before adding the other callers. Deviations from "code MOVED not
+  changed" are named: `|| true` on the ostag capture (a latent abort on every
+  non-Ubuntu host, reproduced), and the `timeout` guard.
+- honors **LRN-070** by never touching the submodule working tree at all. The
+  revision that did (discard, retry, restore) was withdrawn at the gate.
+- honors **LRN-071** (recurrent 3x) by returning the update's real status, not
+  a non-fatal helper's 0.
+- honors **LRN-040** by touching layer 1 only; `GSTACK_CHROMIUM_NO_SANDBOX`
+  is untouched.
+- honors **LRN-085** by keeping the update idempotent, presence-guarded, no
+  `--force`.
+- honors **LRN-036** by putting `$HOME/.bun/bin` on PATH inside the lib.
+- honors **LRN-002** by grepping the moved function name repo-wide, readers
+  included.
+- **LRN-038** already seen: the host-platform override is a dead end.
+- BDR-029's reference line (`decisions.md:544`) and BLK-008's caveat
+  (`blockers.md:118`) describe behavior this plan changes. Registries are
+  append-only, so the plan does NOT edit them: the /feat CAPITALIZE step
+  owns the superseding entry.

.gitignore

@@ -97,6 +97,14 @@ skills-disabled/
 graphify-out/
 .ctx7-cache/
 
+# graphify's vendored skill — written into the repo by `graphify claude
+# install` (install-plugins.sh STEP graphify), since ~/.claude/skills is a
+# symlink to skills/. Untracked so a tool upgrade stops dirtying the tree.
+# test-prompts.json is hand-written for darwin and stays tracked.
+skills/graphify/SKILL.md
+skills/graphify/references/
+skills/graphify/.graphify_version
+
 # /client-handover test artifacts (project-local renders)
 LIVRAISON.md
 LIVRAISON.html

CHANGELOG.md

@@ -6,6 +6,80 @@ Format follows [Keep a Changelog](https://keepachangelog.com/).
 
 ## [Unreleased]
 
+### Added
+- **`make doctor` reports the Playwright browser cache** — a read-only
+  `Playwright browsers` section listing cache size, which registered
+  Playwright install requires each cached browser revision, and counts of
+  unreferenced directories and broken links. Report only: nothing is
+  pruned, since Playwright's own `install` already unions the required set
+  across every registered install.
+- `lib/gstack-playwright.sh` — the gstack Playwright helpers as a shared
+  lib (OS-support bump, submodule-update wrapper, cache report), sourced by
+  `install-plugins.sh`, `update-all.sh` and `doctor.sh`, covered by
+  `lib/tests/gstack-playwright.test.sh`.
+- **`doctor.sh` inspects the `autoMode` block**: warns when a classifier
+  list drops the built-in entries (no `"$defaults"`) and when the
+  user-scope `environment` names a git repo other than the config repo.
+  Neither defect is visible from the deny count, until now the only
+  permission signal `doctor.sh` had.
+- **`templates/settings/SETTINGS.md` documents `autoMode`**: the four
+  classifier lists, `$defaults` splice semantics, `classifyAllShell`, the
+  user-scope vs project-scope rule, and why `ask` is the wrong tier for a
+  destructive command under auto mode.
+
+### Changed
+- **The classifier, not `permissions.ask`, now guards destructive shell
+  work** (BDR-090). Ten rules left the static tiers: `rsync`, `kill -9`,
+  `killall`, `pkill` out of `deny`, and `python3 -c`, `python -c`,
+  `xargs`, `sed`, `cp`, `mv` out of `ask`. Under `defaultMode: auto` an
+  `ask` rule raises no prompt ([[LRN-146]]), so that tier was gating
+  nothing anyway. Cover is now `autoMode.soft_deny`, which the classifier
+  enforces and an explicit instruction clears: writes outside the working
+  directory, `rsync --delete`, SIGKILL and kill-by-name, in-place edits
+  spanning more than one file, directory moves, and inline interpreters
+  or `xargs` that delete or write outside the cwd. Intent clears a soft
+  block for the current turn only.
+- **`autoMode.hard_deny` added** for the three classes no command pattern
+  can express: secret exfiltration (a read and a send, separate steps,
+  possibly turns apart), production deployment (deploy scripts, lftp/FTP
+  pushes, any `prod` target), and disarming the guardrails (weakening a
+  deny list, `--no-verify`, removing the pre-commit hook,
+  `bypassPermissions`). Adding a restriction stays allowed; removing one
+  does not. No instruction clears these.
+
+### Security
+- **Ten secret-reader deny rules added**: `sed`, `awk`, `cut`, `tr`,
+  `sort`, `uniq`, `diff`, `od`, `xxd`, `strings` against `.env*`. Six of
+  those tools sat in `permissions.allow`, so reading a `.env` through
+  them triggered nothing. Same shape and same known gap as the existing
+  `Bash(grep * .env*)` family: a `cat .env | sed` pipe still slips past,
+  which is what the `hard_deny` exfiltration rule is there to catch.
+
+### Fixed
+- **`make update` no longer drops the Playwright OS-support bump** — a
+  gstack submodule update used to leave the bump unapplied until the next
+  `make plugin`, the open caveat of BDR-029. `update-all.sh` now goes
+  through `gstack_submodule_update_with_bump`, which re-applies it after a
+  successful update and returns non-zero on failure so the existing warn
+  arm still fires. Two latent bugs travelled with the extracted code: the
+  ostag capture exited 1 on every non-Ubuntu host and aborted its caller
+  under inherited `errexit`, and the `bun` calls had no timeout.
+- **`autoMode.environment` no longer describes one project from the
+  user-scope file**: the block named a specific repo, its FTP deploy
+  target and its customer data, while `link.sh` symlinks this file to
+  `~/.claude/settings.json` where it reaches every project. The global
+  block now states machine-level facts only (self-hosted Gitea, gitflow
+  protection, `~/.claude/.env` as the single secret source, no CI), and
+  the project-specific facts moved to that project's gitignored
+  `.claude/settings.local.json`. Both lists now open with `"$defaults"`,
+  which the original omitted, so the built-in entries are inherited
+  rather than replaced.
+- `README.md` no longer claims the `ask` tier makes every `mcp__magic__*`
+  call "require a live confirmation and can never auto-execute". That
+  holds under `defaultMode: default`, not under this config's `auto`. The
+  paragraph now separates what is verified from what is not, and names
+  `deny` as the only tier the classifier cannot lift.
+
 ## [1.5.0] — 2026-09-13
 
 ### Added

CLAUDE.md

@@ -30,6 +30,35 @@ install-plugins.sh STEP ctx7 purges it right after; the find-docs skill is
 the single ctx7 surface. If it reappears (manual `ctx7 setup`), delete it
 or re-run `make plugin`.
 
+## Machine-owned: the vendored graphify skill
+
+`skills/graphify/SKILL.md`, `skills/graphify/references/` and
+`.graphify_version` are written by `graphify claude install`
+(`install-plugins.sh` STEP graphify), which lands in the repo because
+`~/.claude/skills` is a symlink to `skills/`. They are gitignored: a
+`pipx upgrade graphifyy` used to dirty the tree and cost a
+`chore(graphify): sync vendored skill X -> Y` commit each time.
+
+Two graphify commands, easy to confuse, and only one restores the skill:
+- `graphify install --platform claude` copies SKILL.md + `references/` +
+  `.graphify_version` into `skills/graphify/`. Touches nothing else.
+  This is the recovery command.
+- `graphify claude install` writes the CLAUDE.md graphify section and the
+  `.claude/settings.json` PreToolUse hooks. It **rewrites both guarded
+  configs** (EVAL-020, verified again 2026-09-15), so revert them after. It does NOT copy
+  the skill.
+
+`make plugin` runs both (`install-plugins.sh` STEP graphify) behind the
+guarded-config EXIT trap, so a fresh clone is covered.
+
+Trade-off accepted: an upstream release can now change the skill's prompt
+with no diff to review. `skills/graphify/test-prompts.json` is hand-written
+for darwin and stays tracked.
+
+Gotcha, learned the hard way: `git rm --cached` keeps the working file,
+but if the branch you merge into still tracks it, the merge deletes it
+from disk. Untrack and merge, then restore with the command above.
+
 ## Transient planning artifacts
 
 `docs/superpowers/specs/**` and `docs/superpowers/plans/**` are run-time

README.md

@@ -300,10 +300,15 @@ check) for up to 10 minutes per call; any local process or open browser tab
 can `POST` to it and that body is injected **verbatim** into the tool result
 the model consumes (job8 audit, `dist/utils/callback-server.js:36`). This is
 in the third-party package's code, not this repo's config — **we don't patch
-it**. The mitigation lives entirely on our side: `settings.json`
+it**. The mitigation lives on our side: `settings.json`
-`permissions.ask` explicitly lists all 4 `mcp__magic__*` tools,
+`permissions.ask` explicitly lists all 4 `mcp__magic__*` tools.
-so every call — builder included — requires a live confirmation and can
+Read that as a declared intent, not a proven hard gate: under
-never auto-execute. Don't allowlist
+`defaultMode: auto` (this config's default) Bash `ask` rules were observed
+auto-approving with no prompt raised (LRN-146). Whether MCP `ask` rules
+behave the same has not been verified here, so re-check before relying on
+it. `deny` is the only tier the auto-mode classifier cannot lift; for a
+gate that holds under auto mode without banning the tool outright, the
+right home is `autoMode.soft_deny`. Don't allowlist
 `21st_magic_component_builder` or `21st_magic_component_refiner` (arbitrary
 absolute-path read → vendor exfil, same audit) under any circumstance.
 
@@ -337,7 +342,7 @@ make profile-reset          # re-enable all gstack skills
 make new-skill name=myskill # scaffold agent + skill files
 ```
 
-`doctor.sh` checks: symlinks, GStack submodule, prerequisites (git, Node, Cargo, Python, Claude Code), plugins, permissions, token budget, config consistency.
+`doctor.sh` checks: symlinks, GStack submodule, Playwright browser cache, prerequisites (git, Node, Cargo, Python, Claude Code), plugins, permissions, token budget, config consistency.
 
 ---
 

doctor.sh

@@ -18,8 +18,10 @@ REPO="$(cd "$(dirname "$0")" && pwd)"
 VERSION=$(cat "$REPO/version.txt" 2>/dev/null || echo "unknown")
 
 # Load shared detection library
-# shellcheck source=lib/detect-plugins.sh
+# shellcheck source=lib/detect-plugins.sh disable=SC1091
 source "$REPO/lib/detect-plugins.sh"
+# shellcheck source=lib/gstack-playwright.sh disable=SC1091
+source "$REPO/lib/gstack-playwright.sh"
 
 echo ""
 echo "═══ claude-config doctor (v${VERSION}) ═══"
@@ -115,6 +117,13 @@ fi
 
 echo ""
 
+# ── Playwright browsers (read-only report; NOT nested under gstack — 2 of
+# the 3 registered installs are gsd-pi, not gstack) ──
+echo "── Playwright browsers ──"
+gstack_browsers_report || true
+
+echo ""
+
 # ────────────────────────────────────────────────────────────
 # 3. Prerequisites
 # ────────────────────────────────────────────────────────────
@@ -206,6 +215,61 @@ echo ""
 # ────────────────────────────────────────────────────────────
 # 5. Permissions check
 # ────────────────────────────────────────────────────────────
+
+# Under defaultMode auto the classifier reads `autoMode`, so a block scoped
+# to ONE project feeds every other project false facts, and a list without
+# "$defaults" silently drops the built-in rules. Neither is visible from the
+# deny count. Emits TAG|message lines for the caller to dispatch.
+inspect_automode() {
+  REPO="$REPO" python3 - "$SETTINGS" <<'PY'
+import json, os, re, sys
+
+settings = json.load(open(sys.argv[1]))
+mode = settings.get("permissions", {}).get("defaultMode")
+block = settings.get("autoMode") or {}
+
+if mode != "auto":
+    sys.exit(print("INFO|defaultMode is %s, autoMode not consulted" % mode))
+if not block:
+    sys.exit(print("WARN|defaultMode is auto but no autoMode block set"))
+
+sections = [k for k in ("allow", "soft_deny", "hard_deny", "environment")
+            if k in block]
+bare = [k for k in sections if "$defaults" not in block[k]]
+if bare:
+    print('WARN|autoMode.%s replaces the built-in entries (no "$defaults")'
+          % ", ".join(bare))
+else:
+    print('PASS|autoMode: %s inherit "$defaults"' % ", ".join(sections))
+
+repo, home = os.environ["REPO"], os.path.expanduser("~")
+foreign = {q for entry in block.get("environment", [])
+           for q in re.findall(r"`(/[^`]+)`", entry)
+           if (p := q.rstrip("/")).startswith(home) and p != repo
+           and os.path.isdir(os.path.join(p, ".git"))}
+if foreign:
+    print("WARN|autoMode.environment names another repo (%s); this file is "
+          "user-scope and reaches every project" % ", ".join(sorted(foreign)))
+else:
+    print("PASS|autoMode.environment is not scoped to a foreign repo")
+PY
+}
+
+check_automode() {
+  local out tag msg
+  if ! out=$(inspect_automode 2>/dev/null); then
+    warn "Could not inspect the autoMode block"
+    return
+  fi
+  while IFS='|' read -r tag msg; do
+    case "$tag" in
+      PASS) pass "$msg" ;;
+      WARN) warn "$msg" ;;
+      INFO) info "$msg" ;;
+    esac
+  done <<< "$out"
+}
+
 echo "── Permissions ──"
 
 SETTINGS="$HOME/.claude/settings.json"
@@ -242,6 +306,8 @@ print(len(json.load(sys.stdin).get('permissions',{}).get('deny',[])))
       warn "Deny rules: $DENY_COUNT (committed: $EXPECTED_DENY) — live settings diverge from last commit"
     fi
   fi
+
+  check_automode
 else
   fail "$HOME/.claude/settings.json not found"
 fi

install-plugins.sh

@@ -26,8 +26,10 @@ else
 fi
 
 # Load shared detection library
-# shellcheck source=lib/detect-plugins.sh
+# shellcheck source=lib/detect-plugins.sh disable=SC1091
 source "$REPO/lib/detect-plugins.sh"
+# shellcheck source=lib/gstack-playwright.sh disable=SC1091
+source "$REPO/lib/gstack-playwright.sh"
 
 # ── Guard hand-curated config against installer drift ────────
 # graphify's installer (Step 7) rewrites CLAUDE.md + .claude/settings.json
@@ -291,35 +293,6 @@ fi
 
 echo ""
 
-# gstack pins Playwright (1.58.x) which only ships browser builds for
-# ubuntu<=24.04. On a newer distro the browser install fails ("does not
-# support chromium on ubuntuXX.04"). Bump gstack's Playwright to a version
-# that supports this OS so ./setup builds the browse binary against it and
-# installs a native browser. Fires only when the pinned version genuinely
-# lacks support — idempotent across runs. Edits the submodule locally (goes
-# dirty); a `git submodule update` resets it and the next install re-applies.
-# See BLK-008 / LRN-040.
-gstack_bump_playwright_if_unsupported() {
-  [ -d "$GSTACK_DIR" ] && [ -r /etc/os-release ] || return 0
-  local ostag pwlib
-  # shellcheck disable=SC1091
-  ostag="$(. /etc/os-release 2>/dev/null; [ "${ID:-}" = ubuntu ] && printf 'ubuntu%s' "${VERSION_ID:-}")"
-  [ -n "$ostag" ] || return 0   # only the known Ubuntu case
-  pwlib="$GSTACK_DIR/node_modules/playwright-core/lib"
-  # populate node_modules at the pinned version so we can read its support list
-  ( cd "$GSTACK_DIR" && { bun install --frozen-lockfile >/dev/null 2>&1 || bun install >/dev/null 2>&1; } ) || return 0
-  if grep -rqs "$ostag" "$pwlib" 2>/dev/null; then
-    return 0   # pinned Playwright already supports this OS
-  fi
-  info "gstack's Playwright lacks $ostag support — bumping to latest (local submodule edit)..."
-  ( cd "$GSTACK_DIR" && bun add playwright@latest >/dev/null 2>&1 )
-  if grep -rqs "$ostag" "$pwlib" 2>/dev/null; then
-    ok "gstack Playwright bumped — now supports $ostag (browse binary rebuilt by ./setup)"
-  else
-    warn "Playwright bump didn't add $ostag support — gstack browser may stay unavailable"
-  fi
-}
-
 # ============================================================
 # STEP 2 — GSTACK SUBMODULE
 # ============================================================
@@ -367,7 +340,8 @@ if [ -d "$GSTACK_DIR" ]; then
   # BEFORE ./setup so its frozen-lockfile install picks up the new version and
   # the browse binary is rebuilt against it (avoids the "does not support
   # chromium" fail). Non-fatal if it can't — gstack is OFF by default.
-  gstack_bump_playwright_if_unsupported
+  # See BLK-008 / LRN-040 / BDR-029; logic lives in lib/gstack-playwright.sh.
+  gstack_bump_playwright_if_unsupported "$GSTACK_DIR"
 
   info "Running GStack setup..."
   _gstack_setup_ok=0

lib/gstack-playwright.sh

@@ -0,0 +1,296 @@
+#!/usr/bin/env bash
+# ============================================================
+# lib/gstack-playwright.sh — gstack's Playwright: OS-support bump +
+# read-only browser-cache report.
+#
+# Sourced by: install-plugins.sh, update-all.sh, doctor.sh — all three run
+# `set -euo pipefail`. gstack_bump_playwright_if_unsupported and
+# gstack_browsers_report are called as BARE STATEMENTS under that inherited
+# errexit, so they `return 0` on every path and every capture that could
+# fail is guarded (`|| true` or an `if`), never a bare `&&`/`||`-less
+# statement. gstack_submodule_update_with_bump is the ONE function allowed
+# to return non-zero — callers use it ONLY as an `if` condition.
+#
+# No `set -euo pipefail` here (mirrors lib/detect-plugins.sh): a sourced
+# lib must not change the caller's shell options.
+#
+# See BDR-029 (bump origin), BLK-008 (Chromium-unsupported-OS saga),
+# LRN-040 (two-layer fix — this file is layer 1 only).
+# ============================================================
+
+_GSPW_GREEN='\033[0;32m'; _GSPW_YELLOW='\033[1;33m'; _GSPW_BLUE='\033[0;34m'
+_GSPW_NC='\033[0m'
+
+_gspw_ok()   { echo -e "  ${_GSPW_GREEN}✓${_GSPW_NC} $1"; }
+_gspw_warn() { echo -e "  ${_GSPW_YELLOW}⚠${_GSPW_NC}  $1"; }
+_gspw_info() { echo -e "  ${_GSPW_BLUE}→${_GSPW_NC} $1"; }
+
+# ── OS support ───────────────────────────────────────────────────────────
+
+# gstack_pw_ostag [os_release_path] — "ubuntu<VERSION_ID>" on Ubuntu, empty
+# otherwise. `|| true` on the capture: the reproduced bug had this exact
+# line abort every non-Ubuntu host under inherited errexit.
+gstack_pw_ostag() {
+  local path="${1:-/etc/os-release}" tag
+  [ -r "$path" ] || return 0
+  # shellcheck disable=SC1090
+  tag="$(. "$path" 2>/dev/null
+    [ "${ID:-}" = ubuntu ] && printf 'ubuntu%s' "${VERSION_ID:-}")" || true
+  if [ -n "$tag" ]; then
+    printf '%s' "$tag"
+  fi
+  return 0
+}
+
+# gstack_pw_supports <playwright_core_lib_dir> <ostag> — 0 supported, 1 not.
+# Always called from an `if`/`&&` context, never as a bare statement.
+gstack_pw_supports() {
+  local pwlib="$1" ostag="$2"
+  [ -n "$ostag" ] && [ -d "$pwlib" ] || return 1
+  grep -rqs "$ostag" "$pwlib" 2>/dev/null
+}
+
+# _gspw_run_timeout <dir> <cmd...> — runs <cmd> in <dir>, under `timeout 300`
+# when available (absent on stock macOS). Exit 124 = the wrapped command was
+# killed by the timeout. Callers MUST invoke this via `cmd || rc=$?` (never
+# bare) so a non-zero exit never trips the caller's inherited errexit.
+_gspw_run_timeout() {
+  local dir="$1"; shift
+  if command -v timeout >/dev/null 2>&1; then
+    ( cd "$dir" && timeout 300 "$@" ) >/dev/null 2>&1
+  else
+    ( cd "$dir" && "$@" ) >/dev/null 2>&1
+  fi
+}
+
+# _gspw_bump_install <gstack_dir> — populate node_modules at the pinned
+# version so its support list can be read. 0 proceed, 1 give up silently
+# (both installs failed, matches the pre-existing silent behavior), 2 give
+# up loud (a timeout truncated node_modules — the support grep would then
+# read a half-written tree).
+_gspw_bump_install() {
+  local dir="$1" rc=0
+  _gspw_run_timeout "$dir" bun install --frozen-lockfile || rc=$?
+  if [ "$rc" -eq 0 ]; then
+    return 0
+  elif [ "$rc" -eq 124 ]; then
+    _gspw_warn "bun install timed out — skipping Playwright bump"
+    return 2
+  fi
+  rc=0
+  _gspw_run_timeout "$dir" bun install || rc=$?
+  if [ "$rc" -eq 0 ]; then
+    return 0
+  elif [ "$rc" -eq 124 ]; then
+    _gspw_warn "bun install timed out — skipping Playwright bump"
+    return 2
+  fi
+  return 1
+}
+
+# _gspw_bump_add_latest <gstack_dir> — 0 ran (support re-checked by caller
+# regardless of bun's own exit code, exactly as the pre-existing code did),
+# 2 timed out (node_modules left half-written — caller must NOT re-check).
+_gspw_bump_add_latest() {
+  local dir="$1" rc=0
+  _gspw_run_timeout "$dir" bun add playwright@latest || rc=$?
+  if [ "$rc" -eq 124 ]; then
+    _gspw_warn "bun add playwright@latest timed out — skipping Playwright bump"
+    return 2
+  fi
+  return 0
+}
+
+# gstack_bump_playwright_if_unsupported <gstack_dir> — BDR-029: bump
+# gstack's pinned Playwright when it lacks a build for this OS, so
+# `./setup` rebuilds the browse binary against a version that has one.
+# OS-gated, idempotent, non-fatal — `return 0` on every path.
+gstack_bump_playwright_if_unsupported() {
+  local gstack_dir="$1" ostag pwlib rc=0
+  [ -d "$gstack_dir" ] && [ -r /etc/os-release ] || return 0
+  ostag="$(gstack_pw_ostag)"
+  [ -n "$ostag" ] || return 0
+  if ! command -v bun >/dev/null 2>&1; then
+    export PATH="$HOME/.bun/bin:$PATH"
+  fi
+  pwlib="$gstack_dir/node_modules/playwright-core/lib"
+  _gspw_info "checking gstack's Playwright OS support ($ostag)..."
+  _gspw_bump_install "$gstack_dir" || rc=$?
+  [ "$rc" -eq 0 ] || return 0
+  if gstack_pw_supports "$pwlib" "$ostag"; then
+    return 0
+  fi
+  _gspw_info "gstack's Playwright lacks $ostag support — bumping to \
+latest (local submodule edit)..."
+  rc=0
+  _gspw_bump_add_latest "$gstack_dir" || rc=$?
+  [ "$rc" -eq 0 ] || return 0
+  if gstack_pw_supports "$pwlib" "$ostag"; then
+    _gspw_ok "gstack Playwright bumped — now supports $ostag (browse \
+binary rebuilt by ./setup)"
+  else
+    _gspw_warn "Playwright bump didn't add $ostag support — gstack \
+browser may stay unavailable"
+  fi
+  return 0
+}
+
+# ── Submodule update ──────────────────────────────────────────────────────
+
+# gstack_submodule_update_with_bump <repo> [sub_path] — the ONE function
+# allowed to return non-zero; callers use it ONLY as an `if` condition.
+# Never touches the submodule working tree: on failure it prints git's own
+# stderr verbatim (never parsed) and returns 1. On success it re-applies
+# the bump (closes BDR-029's caveat: the bump used to survive only until
+# the next `git submodule update`).
+gstack_submodule_update_with_bump() {
+  local repo="$1" sub="${2:-skills-external/gstack}" err rc=0
+  err="$(git -C "$repo" submodule update --remote "$sub" 2>&1 >/dev/null)" \
+    || rc=$?
+  if [ "$rc" -eq 0 ]; then
+    gstack_bump_playwright_if_unsupported "$repo/$sub"
+    return 0
+  fi
+  _gspw_warn "$err"
+  if [ -n "$(git -C "$repo/$sub" status --porcelain \
+      -- package.json bun.lock 2>/dev/null)" ]; then
+    _gspw_info "local Playwright bump (package.json/bun.lock) was not \
+re-applied — re-run: make plugin"
+  fi
+  return 1
+}
+
+# ── Browsers report (read-only) ───────────────────────────────────────────
+
+# _gspw_dir_name_parts <cache_dir_name> — prints "normalized_name revision"
+# split on the LAST '-', mapping '_' -> '-' on the name (Playwright writes
+# chromium_headless_shell-1228 on disk; browsers.json names it
+# chromium-headless-shell).
+_gspw_dir_name_parts() {
+  local rev="${1##*-}" name="${1%-*}"
+  printf '%s %s' "${name//_/-}" "$rev"
+}
+
+# _gspw_browser_referenced <playwright_core_path> <dir_name> — does that
+# install require this cache directory (base revision or any
+# revisionOverrides value)?
+_gspw_browser_referenced() {
+  local json="$1/browsers.json" name rev
+  [ -r "$json" ] || return 1
+  read -r name rev <<< "$(_gspw_dir_name_parts "$2")"
+  awk -F'"' -v want_name="$name" -v want_rev="$rev" '
+    $2 == "name" { cur = $4; in_ov = 0 }
+    $2 == "revision" && !in_ov && cur == want_name && $4 == want_rev {
+      found = 1
+    }
+    $2 == "revisionOverrides" { in_ov = 1 }
+    in_ov && $2 != "revisionOverrides" && cur == want_name \
+      && $4 == want_rev { found = 1 }
+    /^[[:space:]]*}/ { in_ov = 0 }
+    END { exit !found }
+  ' "$json"
+}
+
+# _gspw_browser_name_known <playwright_core_path> <dir_name> — is the NAME
+# listed at all, regardless of revision? (distinguishes "unknown revision"
+# from "unreferenced" in the report.)
+_gspw_browser_name_known() {
+  local json="$1/browsers.json" name rev
+  [ -r "$json" ] || return 1
+  read -r name rev <<< "$(_gspw_dir_name_parts "$2")"
+  awk -F'"' -v want="$name" '$2 == "name" && $4 == want { found = 1 }
+    END { exit !found }' "$json"
+}
+
+# _gspw_install_label <playwright_core_path> — "<dir-before-node_modules>
+# <version>", e.g. "gstack 1.61.1".
+_gspw_install_label() {
+  local pw_path="$1" parent version
+  parent=$(basename "$(dirname "$(dirname "$pw_path")")")
+  version=$(awk -F'"' '$2 == "version" { print $4; exit }' \
+    "$pw_path/package.json" 2>/dev/null) || true
+  printf '%s %s' "$parent" "${version:-?}"
+}
+
+# _gspw_registered_installs <cache_dir> — valid playwright-core paths (dir
+# exists, browsers.json readable), one per line. A `.links` entry whose
+# target is gone or unreadable is silently excluded here (it is counted as
+# a broken link by the caller instead).
+_gspw_registered_installs() {
+  local links_dir="$1/.links" f target
+  [ -d "$links_dir" ] || return 0
+  for f in "$links_dir"/*; do
+    [ -f "$f" ] || continue
+    target=$(cat "$f" 2>/dev/null) || true
+    [ -n "$target" ] || continue
+    if [ -d "$target" ] && [ -r "$target/browsers.json" ]; then
+      printf '%s\n' "$target"
+    fi
+  done
+  return 0
+}
+
+# _gspw_report_dir_line <dir_name> <install_paths_newline_sep> — prints the
+# report line for one cache directory. Returns 1 only when truly
+# unreferenced (caller tallies that); "unknown revision" does not count.
+_gspw_report_dir_line() {
+  local dir_name="$1" installs="$2" p labels="" known=0
+  while IFS= read -r p; do
+    [ -n "$p" ] || continue
+    if _gspw_browser_referenced "$p" "$dir_name"; then
+      labels="${labels:+$labels, }$(_gspw_install_label "$p")"
+    elif _gspw_browser_name_known "$p" "$dir_name"; then
+      known=1
+    fi
+  done <<< "$installs"
+  if [ -n "$labels" ]; then
+    _gspw_info "$dir_name: $labels"
+    return 0
+  elif [ "$known" -eq 1 ]; then
+    _gspw_info "$dir_name: unknown revision"
+    return 0
+  fi
+  _gspw_info "$dir_name: unreferenced"
+  return 1
+}
+
+# gstack_browsers_report [cache_dir] — read-only. `$1` (or
+# PLAYWRIGHT_BROWSERS_PATH, or ~/.cache/ms-playwright) is resolved once;
+# "0" (documented as "bundle into node_modules") and any non-directory
+# degrade to a silent no-cache path. `return 0` on every path.
+gstack_browsers_report() {
+  local cache installs total links_total valid_count broken=0 unref=0 d name
+  cache="${1:-${PLAYWRIGHT_BROWSERS_PATH:-$HOME/.cache/ms-playwright}}"
+  [ "$cache" = "0" ] && return 0
+  [ -d "$cache" ] || return 0
+  installs="$(_gspw_registered_installs "$cache")"
+  links_total=$(find "$cache/.links" -maxdepth 1 -type f 2>/dev/null \
+    | wc -l | tr -d ' ') || true
+  valid_count=$(printf '%s\n' "$installs" | grep -c . || true)
+  broken=$((links_total - valid_count))
+  total=$(du -sh "$cache" 2>/dev/null | awk '{print $1}') || true
+  _gspw_info "Playwright browsers: $cache (${total:-0})"
+  for d in "$cache"/*-[0-9]*; do
+    [ -d "$d" ] || continue
+    name=$(basename "$d")
+    _gspw_report_dir_line "$name" "$installs" || unref=$((unref + 1))
+  done
+  _gspw_info "${unref} unreferenced, ${broken} broken link(s)"
+  if [ "$unref" -gt 0 ] || [ "$broken" -gt 0 ]; then
+    _gspw_warn "unreferenced/broken Playwright browser dirs — re-run \
+\`playwright install\`, which prunes stale revisions"
+  fi
+  return 0
+}
+
+# ── CLI dispatch (only when executed, not sourced) — browsers-report ONLY.
+# The write functions (the bump, the submodule update) stay sourced-only: a
+# CLI verb would expose `bun add playwright@latest` as a command-line entry
+# point. ────────────────────────────────────────────────────────────────
+if [ "${BASH_SOURCE[0]}" = "${0}" ]; then
+  case "${1:-}" in
+    browsers-report) shift; gstack_browsers_report "$@" ;;
+    *) echo "usage: gstack-playwright.sh browsers-report [cache_dir]" >&2
+       exit 2 ;;
+  esac
+fi

lib/tests/gstack-playwright.test.sh

@@ -0,0 +1,213 @@
+#!/usr/bin/env bash
+# lib/tests/gstack-playwright.test.sh — lib/gstack-playwright.sh (T1..T17)
+#
+# git 2.53 defaults protocol.file to "user", which blocks submodule clone
+# and fetch. The fixture git calls alone are not enough: the
+# `git submodule update --remote` under test runs INSIDE the lib, in a
+# fresh git subprocess spawned from THIS process — so the override is
+# exported for the WHOLE test process, not passed per-command.
+set -u
+export GIT_CONFIG_COUNT=1
+export GIT_CONFIG_KEY_0=protocol.file.allow
+export GIT_CONFIG_VALUE_0=always
+
+ROOT="$(cd "$(dirname "$0")/../.." && pwd)"
+L="$ROOT/lib/gstack-playwright.sh"
+pass=0; fail=0
+check() { if [ "$2" = "$3" ]; then pass=$((pass+1)); else fail=$((fail+1));
+  printf 'FAIL %s: got[%s] want[%s]\n' "$1" "$2" "$3"; fi; }
+
+tmp="$(mktemp -d)"; trap 'rm -rf "$tmp"' EXIT
+git_id() { git -C "$1" config user.email t@example.com
+  git -C "$1" config user.name Test; }
+
+# shellcheck source=lib/gstack-playwright.sh
+source "$L"
+
+# ── T1/T2 — ostag detection ──────────────────────────────────────────────
+printf 'ID=ubuntu\nVERSION_ID="24.04"\n' > "$tmp/os-ubuntu"
+printf 'ID=debian\nVERSION_ID="12"\n' > "$tmp/os-debian"
+check T1-ostag-ubuntu "$(gstack_pw_ostag "$tmp/os-ubuntu")" "ubuntu24.04"
+check T2-ostag-other "$(gstack_pw_ostag "$tmp/os-debian")" ""
+
+# ── T3 — errexit safety of the ostag capture (regression: the reproduced
+# bug aborted the whole caller on every non-Ubuntu host) ──
+cat > "$tmp/t3.sh" <<EOF
+#!/usr/bin/env bash
+set -euo pipefail
+source "$L"
+gstack_pw_ostag "$tmp/os-debian"
+echo REACHED
+EOF
+check T3-errexit-safe "$(bash "$tmp/t3.sh" 2>&1 | tail -1)" "REACHED"
+
+# ── T4/T5 — pw_supports, no bun involved ─────────────────────────────────
+mkdir -p "$tmp/pwlib-hit" "$tmp/pwlib-miss"
+echo "supports ubuntu24.04 and others" > "$tmp/pwlib-hit/index.js"
+echo "supports nothing relevant" > "$tmp/pwlib-miss/index.js"
+t4_rc=0; gstack_pw_supports "$tmp/pwlib-hit" ubuntu24.04 >/dev/null 2>&1 \
+  || t4_rc=$?
+check T4-supports-hit "$t4_rc" 0
+t5_rc=0; gstack_pw_supports "$tmp/pwlib-miss" ubuntu24.04 >/dev/null 2>&1 \
+  || t5_rc=$?
+check T5-supports-miss "$t5_rc" 1
+
+# ── T6/T7 — submodule update, real git fixtures ──────────────────────────
+mkdir -p "$tmp/upstream6"
+git -C "$tmp/upstream6" init -q -b main; git_id "$tmp/upstream6"
+printf '{"a":1}\n' > "$tmp/upstream6/package.json"
+git -C "$tmp/upstream6" add package.json
+git -C "$tmp/upstream6" commit -q -m init
+
+mkdir -p "$tmp/repo6"
+git -C "$tmp/repo6" init -q -b main; git_id "$tmp/repo6"
+printf 'x\n' > "$tmp/repo6/README.md"
+git -C "$tmp/repo6" add README.md
+git -C "$tmp/repo6" commit -q -m init
+git -C "$tmp/repo6" -c protocol.file.allow=always \
+  submodule add -q -b main "$tmp/upstream6" gstack-sub
+git -C "$tmp/repo6" config submodule.gstack-sub.branch main
+git -C "$tmp/repo6" commit -q -m "add submodule"
+
+printf 'extra\n' > "$tmp/upstream6/extra.txt"
+git -C "$tmp/upstream6" add extra.txt
+git -C "$tmp/upstream6" commit -q -m "upstream update"
+
+t6_out=$(
+  gstack_bump_playwright_if_unsupported() { echo BUMP_CALLED; }
+  gstack_submodule_update_with_bump "$tmp/repo6" "gstack-sub"
+  echo "rc=$?"
+)
+t6_calls=$(printf '%s\n' "$t6_out" | grep -c BUMP_CALLED)
+t6_rc=$(printf '%s\n' "$t6_out" | grep -o 'rc=[0-9]*')
+check T6-update-success-bumps "$t6_calls:$t6_rc" "1:rc=0"
+
+mkdir -p "$tmp/upstream7"
+git -C "$tmp/upstream7" init -q -b main; git_id "$tmp/upstream7"
+printf '{"a":1}\n' > "$tmp/upstream7/package.json"
+printf 'lockA\n' > "$tmp/upstream7/bun.lock"
+git -C "$tmp/upstream7" add package.json bun.lock
+git -C "$tmp/upstream7" commit -q -m init
+
+mkdir -p "$tmp/repo7"
+git -C "$tmp/repo7" init -q -b main; git_id "$tmp/repo7"
+printf 'x\n' > "$tmp/repo7/README.md"
+git -C "$tmp/repo7" add README.md
+git -C "$tmp/repo7" commit -q -m init
+git -C "$tmp/repo7" -c protocol.file.allow=always \
+  submodule add -q -b main "$tmp/upstream7" gstack-sub
+git -C "$tmp/repo7" config submodule.gstack-sub.branch main
+git -C "$tmp/repo7" commit -q -m "add submodule"
+
+# upstream changes package.json content (would overwrite the local edit)
+printf '{"a":2}\n' > "$tmp/upstream7/package.json"
+git -C "$tmp/upstream7" add package.json
+git -C "$tmp/upstream7" commit -q -m "upstream bumps package.json"
+# local Playwright-bump-style dirty edit, never committed
+printf '{"a":99}\n' > "$tmp/repo7/gstack-sub/package.json"
+
+echo "T7: update-conflict"
+before_pkg=$(cat "$tmp/repo7/gstack-sub/package.json")
+before_lock=$(cat "$tmp/repo7/gstack-sub/bun.lock")
+t7_out=$(gstack_submodule_update_with_bump "$tmp/repo7" "gstack-sub" 2>&1)
+t7_rc=$?
+after_pkg=$(cat "$tmp/repo7/gstack-sub/package.json")
+after_lock=$(cat "$tmp/repo7/gstack-sub/bun.lock")
+t7_files_ok=N
+[ "$before_pkg" = "$after_pkg" ] && [ "$before_lock" = "$after_lock" ] \
+  && t7_files_ok=Y
+t7_hint_ok=N
+printf '%s\n' "$t7_out" | grep -q 'make plugin' && t7_hint_ok=Y
+t7_state="$t7_rc:$t7_files_ok:$t7_hint_ok"
+check T7-update-conflict-nondestructive "$t7_state" "1:Y:Y"
+
+# ── T8 — no destructive command anywhere in the lib source ───────────────
+d8=OK
+sed 's/#.*//' "$L" | grep -qE 'git [^|;]*(checkout|reset|clean|stash)' && d8=BAD
+sed 's/#.*//' "$L" | grep -qwE '(rm|rmdir|unlink|truncate|mv)' && d8=BAD
+check T8-no-destructive-command "$d8" OK
+
+# ── T9-T14 — browsers-report, fixture cache + playwright-core installs ───
+mkdir -p "$tmp/installs/fixA/node_modules/playwright-core"
+cat > "$tmp/installs/fixA/node_modules/playwright-core/browsers.json" <<'EOF'
+{
+  "comment": "Do not edit this file, use utils/roll_browser.js",
+  "browsers": [
+    {
+      "name": "chromium",
+      "revision": "1228",
+      "installByDefault": true
+    },
+    {
+      "name": "chromium-headless-shell",
+      "revision": "1228",
+      "installByDefault": true
+    },
+    {
+      "name": "webkit",
+      "revision": "2311",
+      "installByDefault": true,
+      "revisionOverrides": {
+        "mac14": "2251",
+        "debian11-x64": "2105"
+      }
+    },
+    {
+      "name": "ffmpeg",
+      "revision": "1011",
+      "installByDefault": true
+    }
+  ]
+}
+EOF
+cat > "$tmp/installs/fixA/node_modules/playwright-core/package.json" <<'EOF'
+{
+  "name": "playwright-core",
+  "version": "1.61.1"
+}
+EOF
+
+mkdir -p "$tmp/cache1/.links" \
+  "$tmp/cache1/chromium-1228" \
+  "$tmp/cache1/chromium_headless_shell-1228" \
+  "$tmp/cache1/webkit-2105" \
+  "$tmp/cache1/firefox-9999" \
+  "$tmp/cache1/chromium-9999"
+printf '%s' "$tmp/installs/fixA/node_modules/playwright-core" \
+  > "$tmp/cache1/.links/link-valid"
+printf '%s' "$tmp/no-such-install/node_modules/playwright-core" \
+  > "$tmp/cache1/.links/link-broken"
+
+out1="$(gstack_browsers_report "$tmp/cache1" 2>&1)"
+has1() { printf '%s\n' "$out1" | grep -q "$1" && echo Y; }
+check T9-report-referenced "$(has1 'chromium-1228: fixA 1.61.1')" Y
+check T10-report-underscore-dir \
+  "$(has1 'chromium_headless_shell-1228: fixA 1.61.1')" Y
+t11_unref=$(has1 'firefox-9999: unreferenced')
+t11_unknown=$(has1 'chromium-9999: unknown revision')
+check T11-report-unreferenced "$t11_unref$t11_unknown" YY
+check T12-report-broken-link "$(has1 '1 broken link')" Y
+check T13-report-revision-override "$(has1 'webkit-2105: fixA 1.61.1')" Y
+
+mkdir -p "$tmp/cache2/.links" "$tmp/cache2/chromium-1228"
+printf '%s' "$tmp/installs/fixA/node_modules/playwright-core" \
+  > "$tmp/cache2/.links/link-valid"
+out2="$(gstack_browsers_report "$tmp/cache2" 2>&1)"; rc2=$?
+zero2=$(printf '%s\n' "$out2" | grep -q '0 unreferenced, 0 broken link(s)' \
+  && echo Y)
+check T14-report-zero-counts-exit-0 "$rc2:$zero2" "0:Y"
+
+# ── T15/T16 — degrade silently, nothing on stderr ────────────────────────
+err15="$(gstack_browsers_report "$tmp/does-not-exist-cache" 2>&1 1>/dev/null)"
+rc15=$?
+check T15-report-no-cache "$rc15:[$err15]" "0:[]"
+
+err16="$(gstack_browsers_report "0" 2>&1 1>/dev/null)"
+rc16=$?
+check T16-report-browsers-path-zero "$rc16:[$err16]" "0:[]"
+
+# ── T17 — sourcing emits nothing ──────────────────────────────────────────
+out17="$(bash -c "source '$L'; :" 2>&1)"
+check T17-source-safe "[$out17]" "[]"
+
+printf 'PASS=%s FAIL=%s\n' "$pass" "$fail"; [ "$fail" -eq 0 ]

settings.json

@@ -110,12 +110,8 @@
       "Bash(chmod -R 777 *)",
       "Bash(ssh *)",
       "Bash(scp *)",
-      "Bash(rsync *)",
       "Bash(nc *)",
       "Bash(netcat *)",
-      "Bash(kill -9 *)",
-      "Bash(killall *)",
-      "Bash(pkill *)",
       "Bash(crontab *)",
       "Bash(systemctl *)",
       "Bash(service *)",
@@ -182,6 +178,16 @@
       "Bash(more .env.*)",
       "Bash(grep * .env)",
       "Bash(grep * .env.*)",
+      "Bash(sed * .env*)",
+      "Bash(awk * .env*)",
+      "Bash(cut * .env*)",
+      "Bash(tr * .env*)",
+      "Bash(sort * .env*)",
+      "Bash(uniq * .env*)",
+      "Bash(diff * .env*)",
+      "Bash(od * .env*)",
+      "Bash(xxd * .env*)",
+      "Bash(strings * .env*)",
       "Bash(env)",
       "Bash(printenv)",
       "Bash(printenv *)",
@@ -219,8 +225,6 @@
       "Bash(wget * | sh)",
       "Bash(mkfifo *)",
       "Bash(node -e *)",
-      "Bash(python3 -c *)",
-      "Bash(python -c *)",
       "Bash(git push *)",
       "Bash(git push)",
       "Bash(docker run *)",
@@ -234,10 +238,6 @@
       "Bash(pacman -S *)",
       "WebSearch",
       "WebFetch",
-      "Bash(xargs *)",
-      "Bash(sed *)",
-      "Bash(cp *)",
-      "Bash(mv *)",
       "Bash(git stash pop*)",
       "Bash(git stash drop*)",
       "Bash(git stash clear)",
@@ -358,5 +358,40 @@
   "effortLevel": "xhigh",
   "remoteControlAtStartup": true,
   "inputNeededNotifEnabled": true,
-  "skipAutoPermissionPrompt": true
+  "skipAutoPermissionPrompt": true,
+  "autoMode": {
+    "soft_deny": [
+      "$defaults",
+      "Scope of intent: an instruction clears a SOFT BLOCK for the current turn only. An approval given in an earlier turn is not an approval now, and the same action repeated in a later turn has to be asked for again.",
+      "Writing outside the current working directory: `cp`, `mv`, `sed -i`, `rsync`, `tee`, or a shell redirection whose destination resolves outside the cwd. Several sibling projects live under `~/Documents/`, so the realistic failure is writing into the wrong one, where git recovers nothing. Clear only when the user named the destination in this turn.",
+      "`rsync` invoked with `--delete`. It removes files at the destination that are absent from the source, with no undo. Clear only against a destination the user named in this turn.",
+      "Sending SIGKILL (`kill -9`) or killing processes by name (`killall`, `pkill`). These reach processes outside this session, including the user's editors, shells, dtach sessions and background jobs, and the target is chosen by a pattern, so a typo kills the wrong thing. Clear only when the user named the process in this turn.",
+      "Editing more than one file in place in a single command: `sed -i` or `perl -pi` over a glob, or a loop over `git ls-files`. The damage is not loss, since git recovers it, but a diff spanning hundreds of files that nobody reads before committing. `sed -i` on a single named file passes. Clear only when the user asked for the sweep.",
+      "Moving or renaming a directory inside the repo (`mv src/api src/api_old`, or any `mv` of a tree). It breaks imports and paths silently, and the breakage surfaces far from the command. Clear only when the user asked for that move.",
+      "An inline interpreter or `xargs` that deletes, or that writes outside the current working directory: `python3 -c`, `python -c` or `node -e` calling `rmtree`, `remove`, `unlink` or `truncate`; `xargs` feeding `rm`, `mv` or `dd`. `find ... | xargs rm` is the case that matters, since it routes around the `find * -exec rm` deny rule. Reading, computing, and editing a file inside the working directory pass untouched."
+    ],
+    "hard_deny": [
+      "$defaults",
+      "Secret exfiltration: reading a `.env`, an SSH key, a token or a credentials file, and then sending what it contained outside this machine. That covers an HTTP request body or header, a paste or gist service, a file upload, an email, and a commit or push to any repository. The static deny rules match the reading tools by pattern and cannot see the second half of the chain; read and send are separate steps and may sit several turns apart. No instruction clears this.",
+      "Production deployment: running a project's deploy script (`bin/deploy.sh` and its equivalents), any lftp, FTP, SFTP or rsync push to a hosting provider, and any action against a target whose name carries `prod` or `production` as a whole word or name segment. The user deploys by hand, out of session. A green test suite, a finished feature, or a plan step that reads \"deploy\" is not an instruction to deploy. No in-session instruction clears this.",
+      "Disarming the guardrails: removing or weakening an entry in the `deny`, `soft_deny` or `hard_deny` lists of any settings.json, passing `--no-verify` to git, deleting or chmod-ing `.githooks/pre-commit`, setting `disableAllHooks`, or switching `permissions.defaultMode` to `bypassPermissions`. Adding a restriction is fine; removing one is not. When a task is blocked by a guardrail, say so and stop, rather than widening the guardrail to get through. The user maintains these files by hand. No instruction clears this."
+    ],
+    "environment": [
+      "$defaults",
+      "### Machine-specific (refines any \"None configured\" default above)",
+      "**Primary use of Claude Code**: software development on a personal Linux workstation. Single developer, no organization.",
+      "**Source control**: self-hosted Gitea at `git.bchanot.fr` (SSH on port 49220). Some checkouts under `/home/bchanot/Documents/` have no remote at all and are local-only.",
+      "**Repository visibility**: private. The Gitea instance is self-hosted and not publicly indexed, and a checkout with no remote is local-only. Treat every repo here as private unless its remote points at a public host.",
+      "**Trusted repo**: the checkout Claude Code is currently working in, under `/home/bchanot/Documents/`. No single repo is privileged over the others — read the current one, do not assume a previous session's project.",
+      "**Trusted internal domains**: `git.bchanot.fr` (self-hosted Gitea). It is the only internal service.",
+      "**Default / protected branches**: gitflow. `main` (prod) and `develop` (integration) are protected: a per-repo pre-commit hook refuses code commits on either (exempting `.claude/**` and merges) and Gitea enforces branch protection on both. Work lands on `feature/*`, `bugfix/*`, `chore/*`, `release/*`, `hotfix/*`.",
+      "**Secrets management**: `~/.claude/.env` is the single source of truth and lives outside every git tree; repos reach it through a gitignored symlink. Only `.env.example`, holding placeholders, is ever tracked. A real secret inside a repo is a defect, not a configuration.",
+      "**Internal sharing / snippet hosting**: none. Public paste, gist and pastebin services are outside the trust boundary.",
+      "**CI/CD deploy targets**: no CI system. Deploys run out of band from a per-project runbook, typically lftp/FTP to OVH mutualised hosting for web projects. Nothing deploys automatically on a push or a merge.",
+      "**Internal package registry**: none. Public npm and PyPI.",
+      "**Host containment**: an ordinary developer workstation with open internet and no sandbox. Nothing is contained by the environment itself.",
+      "**Sensitive remote targets**: any namespace, host, database or container whose name carries `prod` or `production` as a whole word or name segment.",
+      "**Sensitive data locations & audiences**: per-project `.env` files (gitignored) hold database, deploy and API credentials; some web projects store customer-submitted form data under a retention policy. Both are personal or client data — never send either to an external service."
+    ]
+  }
 }

skills/graphify/.graphify_version

@@ -1 +0,0 @@
-0.9.15

skills/graphify/SKILL.md

@@ -1,678 +0,0 @@
----
-name: graphify
-description: "Use for any question about a codebase, its architecture, file relationships, or project content — especially when graphify-out/ exists, where the question should be treated as a graphify query first. Turns any input (code, docs, papers, images, videos) into a persistent knowledge graph with god nodes, community detection, and query/path/explain tools."
----
-
-# /graphify
-
-Turn any folder of files into a navigable knowledge graph with community detection, an honest audit trail, and three outputs: interactive HTML, GraphRAG-ready JSON, and a plain-language GRAPH_REPORT.md.
-
-## Usage
-
-```
-/graphify                                             # full pipeline on current directory (HTML viz; add --obsidian for a vault)
-/graphify <path>                                      # full pipeline on specific path
-/graphify https://github.com/<owner>/<repo>           # clone repo then run full pipeline on it
-/graphify https://github.com/<owner>/<repo> --branch <branch>  # clone a specific branch
-/graphify <url1> <url2> ...                           # clone multiple repos, build each, merge into one cross-repo graph
-/graphify <path> --mode deep                          # thorough extraction, richer INFERRED edges
-/graphify <path> --update                             # incremental - re-extract only new/changed files
-/graphify <path> --directed                            # build directed graph (preserves edge direction: source→target)
-/graphify <path> --whisper-model medium                # use a larger Whisper model for better transcription accuracy
-/graphify <path> --cluster-only                       # rerun clustering on existing graph
-/graphify <path> --no-viz                             # skip visualization, just report + JSON
-/graphify <path> --html                               # (HTML is generated by default - this flag is a no-op)
-/graphify <path> --svg                                # also export graph.svg (embeds in Notion, GitHub)
-/graphify <path> --graphml                            # export graph.graphml (Gephi, yEd)
-/graphify <path> --neo4j                              # generate graphify-out/cypher.txt for Neo4j
-/graphify <path> --neo4j-push bolt://localhost:7687   # push directly to Neo4j
-/graphify <path> --falkordb                           # generate graphify-out/cypher.txt for FalkorDB
-/graphify <path> --falkordb-push falkordb://localhost:6379   # push directly to FalkorDB
-/graphify <path> --mcp                                # start MCP stdio server for agent access
-/graphify <path> --watch                              # watch folder, auto-rebuild on code changes (no LLM needed)
-/graphify <path> --wiki                               # build agent-crawlable wiki (index.md + one article per community)
-/graphify <path> --obsidian --obsidian-dir ~/vaults/my-project  # write vault to custom path (e.g. existing vault)
-/graphify add <url>                                   # fetch URL, save to ./raw, update graph
-/graphify add <url> --author "Name"                   # tag who wrote it
-/graphify add <url> --contributor "Name"              # tag who added it to the corpus
-/graphify query "<question>"                          # BFS traversal - broad context
-/graphify query "<question>" --dfs                    # DFS - trace a specific path
-/graphify query "<question>" --budget 1500            # cap answer at N tokens
-/graphify path "AuthModule" "Database"                # shortest path between two concepts
-/graphify explain "SwinTransformer"                   # plain-language explanation of a node
-```
-
-## What graphify is for
-
-Drop any folder of code, docs, papers, images, or video into graphify and get a queryable knowledge graph. Persistent across sessions, honest audit trail (EXTRACTED/INFERRED/AMBIGUOUS), community detection surfaces cross-document connections you wouldn't think to ask about.
-
-## What You Must Do When Invoked
-
-If the user invoked `/graphify --help` or `/graphify -h` (with no other arguments), print the contents of the `## Usage` section above verbatim and stop. Do not run any commands, do not detect files, do not default the path to `.`. Just print the Usage block and return.
-
-**Fast path — existing graph:** Before doing anything else, check whether `graphify-out/graph.json` exists. The expected location is `graphify-out/graph.json` relative to the **current working directory** (i.e. the project root where you are running commands). If it exists AND the user's request is a natural-language question about the codebase (e.g. "How does X work?", "What calls Y?", "Trace the data flow through Z") and NOT an explicit rebuild command (`--update`, `--cluster-only`, or a bare path/URL that implies fresh extraction): **skip Steps 1–5 entirely and jump straight to `## For /graphify query`.** Run `graphify query "<question>"` immediately. Do not run detect. Do not check corpus size. Do not ask the user to narrow. The graph is already built — use it.
-
-If no path was given, use `.` (current directory). Do not ask the user for a path.
-
-If the path argument starts with `https://github.com/` or `http://github.com/`, treat it as a GitHub URL - run Step 0 before anything else, then continue with the resolved local path.
-
-Follow these steps in order. Do not skip steps.
-
-### Step 0 - GitHub repos and multi-path merge (only if a URL or several paths)
-
-Only when the path is one or more `https://github.com/...` URLs, or several local subfolders to merge. See `references/github-and-merge.md` for the clone, cross-repo merge, and monorepo flow, then continue with the resolved local path. A plain local path skips this step.
-
-### Step 1 - Ensure graphify is installed
-
-```bash
-# Detect the correct Python interpreter (handles uv tool, pipx, venv, system installs)
-PYTHON=""
-GRAPHIFY_BIN=$(which graphify 2>/dev/null)
-# 1. uv tool installs — most reliable on modern Mac/Linux
-if [ -z "$PYTHON" ] && command -v uv >/dev/null 2>&1; then
-    _UV_PY=$(uv tool run --from graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
-    if [ -n "$_UV_PY" ]; then PYTHON="$_UV_PY"; fi
-fi
-# 2. Read shebang from graphify binary (pipx and direct pip installs)
-if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
-    _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
-    case "$_SHEBANG" in
-        *[!a-zA-Z0-9/_.@-]*) ;;
-        *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
-    esac
-fi
-# 3. Fall back to python3
-if [ -z "$PYTHON" ]; then PYTHON="python3"; fi
-if ! "$PYTHON" -c "import graphify" 2>/dev/null; then
-    if command -v uv >/dev/null 2>&1; then
-        uv tool install --upgrade graphifyy -q 2>&1 | tail -3
-        _UV_PY=$(uv tool run --from graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
-        if [ -n "$_UV_PY" ]; then PYTHON="$_UV_PY"; fi
-    else
-        "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
-          || "$PYTHON" -m pip install graphifyy -q --break-system-packages 2>&1 | tail -3
-    fi
-fi
-# Write interpreter path for all subsequent steps (persists across invocations)
-mkdir -p graphify-out
-"$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
-# Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
-```
-
-If the import succeeds, print nothing and move straight to Step 2.
-
-**In every subsequent bash block, replace `python3` with `$(cat graphify-out/.graphify_python)` to use the correct interpreter.**
-
-### Step 2 - Detect files
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from graphify.detect import detect
-from pathlib import Path
-result = detect(Path('INPUT_PATH'))
-print(json.dumps(result, ensure_ascii=False))
-" > graphify-out/.graphify_detect.json
-```
-
-Replace INPUT_PATH with the actual path the user provided. Do NOT cat or print the JSON - read it silently and present a clean summary instead:
-
-```
-Corpus: X files · ~Y words
-  code:     N files (.py .ts .go ...)
-  docs:     N files (.md .txt ...)
-  papers:   N files (.pdf ...)
-  images:   N files
-  video:    N files (.mp4 .mp3 ...)
-```
-
-Omit any category with 0 files from the summary.
-
-Then act on it:
-- If `total_files` is 0: stop with "No supported files found in [path]."
-- If `skipped_sensitive` is non-empty: mention file count skipped, not the file names.
-- If `total_words` > 2,000,000 OR `total_files` > 500: show the warning. Then compute the top 5 first-level subdirectories by file count:
-  - Read `scan_root` from the detect JSON (always an absolute path to the resolved INPUT_PATH).
-  - Concatenate all file lists across all types (`code`, `document`, `paper`, `image`, `video`).
-  - Filter out any path that starts with `scan_root + "/graphify-out/"` to exclude converted sidecars.
-  - For each file, strip the `scan_root` prefix and take the first path component. Files directly in `scan_root` with no subdirectory count as `(root)`.
-  - If all files are in `(root)` with no subdirectories, do not ask to narrow — no subfolders exist. Instead suggest `--no-cluster` to skip the expensive clustering step and proceed.
-  - Otherwise rank by count, show the top 5 with file counts, then ask which subfolder to run on. Wait for the user's answer before proceeding.
-- Otherwise: proceed directly to Step 2.5 if video files were detected, or Step 3 if not.
-
-### Step 2.5 - Video and audio (only if video files detected)
-
-Skip this step entirely if `detect` returned zero `video` files. When the corpus has video or audio, see `references/transcribe.md` to transcribe them to text first, then treat the transcripts as doc files in Step 3.
-
-### Step 3 - Extract entities and relationships
-
-**Before starting:** note whether `--mode deep` was given. You must pass `DEEP_MODE=true` to every subagent in Step B2 if it was. Track this from the original invocation - do not lose it.
-
-This step has two parts: **structural extraction** (deterministic, free) and **semantic extraction** (LLM, costs tokens).
-
-> **graphify needs no API key. Never ask the user for one, and never block on one.** Code is extracted structurally (AST) with no LLM and no key at all — a code-only corpus (the common `/graphify .` on a repo) skips semantic extraction entirely, so it needs nothing here: go straight to Part A and skip Part B. Semantic extraction (only for docs, papers, and images) uses Gemini **only if** `GEMINI_API_KEY`/`GOOGLE_API_KEY` is already set; otherwise the host agent itself is the LLM. graphify does **not** read `ANTHROPIC_API_KEY`, `OPENAI_API_KEY`, or any other provider key. If you catch yourself about to prompt for, wait on, or stop because of a missing API key, that is a misread of this skill — proceed without one.
-
-**Before semantic extraction:** check whether `GEMINI_API_KEY` or `GOOGLE_API_KEY` is set. If neither is set, print this one-liner to the user:
-> Tip: set `GEMINI_API_KEY` or `GOOGLE_API_KEY` to use Gemini for semantic extraction (`pip install 'graphifyy[gemini]'`).
-
-Print it once, then continue — do not wait for the user to supply a key. If `GEMINI_API_KEY` or `GOOGLE_API_KEY` IS set, use `graphify.llm.extract_corpus_parallel(files, backend="gemini")` for semantic extraction instead of dispatching subagents. The default Gemini model is `gemini-3-flash-preview`; set `GRAPHIFY_GEMINI_MODEL` or pass `--model` in headless CLI flows to override it.
-
-> **No other API keys are read.** When `GEMINI_API_KEY`/`GOOGLE_API_KEY` are unset, semantic extraction falls to the host agent itself — the running session is the LLM. On a host that dispatches subagents (e.g. Claude Code), dispatch them as written in Part B. On a host that runs the CLI directly in a terminal and cannot dispatch subagents, do not stall: a code-only corpus has no semantic work, so write the empty semantic file (Part B "Fast path") and continue to Part C; for a corpus with docs/papers/images, either set a Gemini key or extract those inline yourself, but in no case prompt for `ANTHROPIC_API_KEY` — that prompt is a misread of this skill.
-
-**Run Part A (AST) and Part B (semantic) in parallel. Dispatch all semantic subagents AND start AST extraction in the same message. Both can run simultaneously since they operate on different file types. Merge results in Part C as before.**
-
-Note: Parallelizing AST + semantic saves 5-15s on large corpora. AST is deterministic and fast; start it while subagents are processing docs/papers.
-
-#### Part A - Structural extraction for code files
-
-For any code files detected, run AST extraction in parallel with Part B subagents:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import sys, json
-from graphify.extract import collect_files, extract
-from pathlib import Path
-import json
-
-code_files = []
-detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
-for f in detect.get('files', {}).get('code', []):
-    code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
-
-if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
-    Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
-    print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
-else:
-    Path('graphify-out/.graphify_ast.json').write_text(json.dumps({'nodes':[],'edges':[],'input_tokens':0,'output_tokens':0}, ensure_ascii=False), encoding=\"utf-8\")
-    print('No code files - skipping AST extraction')
-"
-```
-
-#### Part B - Semantic extraction (parallel subagents)
-
-**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from pathlib import Path
-Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
-"
-```
-
-**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
-
-Before dispatching subagents, print a timing estimate:
-- Load `total_words` and file counts from `graphify-out/.graphify_detect.json`
-- Estimate agents needed: `ceil(uncached_non_code_files / 22)` (chunk size is 20-25)
-- Estimate time: ~45s per agent batch (they run in parallel, so total ≈ 45s × ceil(agents/parallel_limit))
-- Print: "Semantic extraction: ~N files → X agents, estimated ~Ys"
-
-**Step B0 - Check extraction cache first**
-
-Before dispatching any subagents, check which files already have cached extraction results:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from graphify.cache import check_semantic_cache
-from pathlib import Path
-
-detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
-# Only content files go to semantic extraction. Code is already covered structurally
-# by the AST pass (Part A); flattening every category here makes subagents re-read
-# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
-all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
-
-cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
-
-# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
-# run so Part C never merges a stale .graphify_cached.json (#1392).
-if cached_nodes or cached_edges or cached_hyperedges:
-    Path('graphify-out/.graphify_cached.json').write_text(json.dumps({'nodes': cached_nodes, 'edges': cached_edges, 'hyperedges': cached_hyperedges}, ensure_ascii=False), encoding=\"utf-8\")
-else:
-    Path('graphify-out/.graphify_cached.json').unlink(missing_ok=True)
-Path('graphify-out/.graphify_uncached.txt').write_text('\n'.join(uncached), encoding=\"utf-8\")
-print(f'Cache: {len(all_files)-len(uncached)} files hit, {len(uncached)} files need extraction')
-"
-```
-
-Only dispatch subagents for files listed in `graphify-out/.graphify_uncached.txt`. If all files are cached, skip to Part C directly.
-
-**Step B1 - Split into chunks**
-
-Load files from `graphify-out/.graphify_uncached.txt`. Split into chunks of 20-25 files each. Each image gets its own chunk (vision needs separate context). When splitting, group files from the same directory together so related artifacts land in the same chunk and cross-file relationships are more likely to be extracted.
-
-**Step B2 - Dispatch ALL subagents in a single message**
-
-Call the Agent tool multiple times IN THE SAME RESPONSE - one call per chunk. This is the only way they run in parallel. If you make one Agent call, wait, then make another, you are doing it sequentially and defeating the purpose.
-
-**IMPORTANT - subagent type:** Always use `subagent_type="general-purpose"`. Do NOT use `Explore` - it is read-only and cannot write chunk files to disk, which silently drops extraction results. General-purpose has Write and Bash access which the subagent needs.
-
-Concrete example for 3 chunks:
-```
-[Agent tool call 1: files 1-15, subagent_type="general-purpose"]
-[Agent tool call 2: files 16-30, subagent_type="general-purpose"]
-[Agent tool call 3: files 31-45, subagent_type="general-purpose"]
-```
-All three in one message. Not three separate messages.
-
-Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL_CHUNKS, DEEP_MODE, and CHUNK_PATH).
-
-CHUNK_PATH must be an **absolute** path — derive it before dispatching:
-```bash
-PROJECT_ROOT=$(pwd)  # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
-# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
-```
-
-Subagent prompt template:
-
-See `references/extraction-spec.md` for the exact subagent prompt (JSON schema, node-ID rules, confidence rubric, frontmatter, hyperedge, and vision rules). Load it only here, only when at least one chunk holds a doc, paper, or image; a pure-code corpus has skipped Part B and never reads it. Pass each subagent that prompt verbatim with FILE_LIST, CHUNK_NUM, TOTAL_CHUNKS, DEEP_MODE, and CHUNK_PATH substituted, and have it write the result to CHUNK_PATH.
-
-**Step B3 - Collect, cache, and merge**
-
-Wait for all subagents. For each result:
-- Check that `graphify-out/.graphify_chunk_NN.json` exists on disk — this is the success signal
-- If the file exists and contains valid JSON with `nodes` and `edges`, include it and save to cache
-- If the file is missing, the subagent was likely dispatched as read-only (Explore type) — print a warning: "chunk N missing from disk — subagent may have been read-only. Re-run with general-purpose agent." Do not silently skip.
-- If a subagent failed or returned invalid JSON, print a warning and skip that chunk - do not abort
-
-If more than half the chunks failed or are missing, stop and tell the user to re-run and ensure `subagent_type="general-purpose"` is used.
-
-Merge all chunk files into `.graphify_semantic_new.json`. **After each Agent call completes, read the real token counts from the Agent tool result's `usage` field and write them back into the chunk JSON before merging** — the chunk JSON itself always has placeholder zeros. Then run:
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json, glob
-from pathlib import Path
-
-chunks = sorted(glob.glob('graphify-out/.graphify_chunk_*.json'))
-all_nodes, all_edges, all_hyperedges = [], [], []
-total_in, total_out = 0, 0
-for c in chunks:
-    d = json.loads(Path(c).read_text(encoding=\"utf-8\"))
-    all_nodes += d.get('nodes', [])
-    all_edges += d.get('edges', [])
-    all_hyperedges += d.get('hyperedges', [])
-    total_in += d.get('input_tokens', 0)
-    total_out += d.get('output_tokens', 0)
-Path('graphify-out/.graphify_semantic_new.json').write_text(json.dumps({
-    'nodes': all_nodes, 'edges': all_edges, 'hyperedges': all_hyperedges,
-    'input_tokens': total_in, 'output_tokens': total_out,
-}, indent=2, ensure_ascii=False), encoding=\"utf-8\")
-print(f'Merged {len(chunks)} chunks: {total_in:,} in / {total_out:,} out tokens')
-"
-```
-
-Save new results to cache:
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from graphify.cache import save_semantic_cache
-from pathlib import Path
-
-new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
-uncached = [line for line in Path('graphify-out/.graphify_uncached.txt').read_text(encoding=\"utf-8\").splitlines() if line]
-saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH', allowed_source_files=uncached)
-print(f'Cached {saved} files')
-"
-```
-
-Merge cached + new results into `graphify-out/.graphify_semantic.json`:
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from pathlib import Path
-
-cached = json.loads(Path('graphify-out/.graphify_cached.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_cached.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
-new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
-
-all_nodes = cached['nodes'] + new.get('nodes', [])
-all_edges = cached['edges'] + new.get('edges', [])
-all_hyperedges = cached.get('hyperedges', []) + new.get('hyperedges', [])
-seen = set()
-deduped = []
-for n in all_nodes:
-    if n['id'] not in seen:
-        seen.add(n['id'])
-        deduped.append(n)
-
-merged = {
-    'nodes': deduped,
-    'edges': all_edges,
-    'hyperedges': all_hyperedges,
-    'input_tokens': new.get('input_tokens', 0),
-    'output_tokens': new.get('output_tokens', 0),
-}
-Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
-print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
-"
-```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
-
-#### Part C - Merge AST + semantic into final extraction
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import sys, json
-from pathlib import Path
-
-ast = json.loads(Path('graphify-out/.graphify_ast.json').read_text(encoding=\"utf-8\"))
-sem = json.loads(Path('graphify-out/.graphify_semantic.json').read_text(encoding=\"utf-8\"))
-
-# Merge: AST nodes first, semantic nodes deduplicated by id
-seen = {n['id'] for n in ast['nodes']}
-merged_nodes = list(ast['nodes'])
-for n in sem['nodes']:
-    if n['id'] not in seen:
-        merged_nodes.append(n)
-        seen.add(n['id'])
-
-merged_edges = ast['edges'] + sem['edges']
-merged_hyperedges = sem.get('hyperedges', [])
-merged = {
-    'nodes': merged_nodes,
-    'edges': merged_edges,
-    'hyperedges': merged_hyperedges,
-    'input_tokens': sem.get('input_tokens', 0),
-    'output_tokens': sem.get('output_tokens', 0),
-}
-Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
-total = len(merged_nodes)
-edges = len(merged_edges)
-print(f'Merged: {total} nodes, {edges} edges ({len(ast[\"nodes\"])} AST + {len(sem[\"nodes\"])} semantic)')
-"
-```
-
-### Step 4 - Build graph, cluster, analyze, generate outputs
-
-**Before starting:** the code blocks below pass `directed=IS_DIRECTED` to `build_from_json()`. Replace `IS_DIRECTED` with `True` if `--directed` was given (builds a `DiGraph` preserving edge direction source→target), otherwise `False` (the default undirected `Graph`). Substitute it the same way you substitute `INPUT_PATH` — do not leave the literal `IS_DIRECTED` in the code.
-
-```bash
-mkdir -p graphify-out
-$(cat graphify-out/.graphify_python) -c "
-import sys, json
-from graphify.build import build_from_json
-from graphify.cluster import cluster, score_all
-from graphify.analyze import god_nodes, surprising_connections, suggest_questions
-from graphify.report import generate
-from graphify.export import to_json
-from pathlib import Path
-
-extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
-detection  = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
-
-# root= mirrors the --update runbook (#1361): relativize source_file to the same
-# base so the full build and incremental --update never drift apart on re-extract.
-G = build_from_json(extraction, root='INPUT_PATH', directed=IS_DIRECTED)
-# Guard BEFORE any write: an empty extraction must not clobber a good graph.json /
-# GRAPH_REPORT.md / analysis sidecar. Check immediately after build (#1392).
-if G.number_of_nodes() == 0:
-    print('ERROR: Graph is empty - extraction produced no nodes.')
-    print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
-    raise SystemExit(1)
-communities = cluster(G)
-cohesion = score_all(G, communities)
-tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
-gods = god_nodes(G)
-surprises = surprising_connections(G, communities)
-labels = {cid: 'Community ' + str(cid) for cid in communities}
-# Placeholder questions - regenerated with real labels in Step 5
-questions = suggest_questions(G, communities, labels)
-
-# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
-# nothing) when the new graph is smaller than the existing graph.json. Only write
-# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
-# they never describe a graph that graph.json doesn't contain (#1392).
-wrote = to_json(G, communities, 'graphify-out/graph.json')
-if not wrote:
-    print('ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).')
-    print('If this shrink is intentional (you deleted files), re-run a full build with --force.')
-    raise SystemExit(1)
-report = generate(G, communities, cohesion, labels, gods, surprises, detection, tokens, 'INPUT_PATH', suggested_questions=questions)
-Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
-analysis = {
-    'communities': {str(k): v for k, v in communities.items()},
-    'cohesion': {str(k): v for k, v in cohesion.items()},
-    'gods': gods,
-    'surprises': surprises,
-    'questions': questions,
-}
-Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
-print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
-"
-```
-
-If this step prints `ERROR: Graph is empty`, stop and tell the user what happened - do not proceed to labeling or visualization.
-
-Replace INPUT_PATH with the actual path.
-
-### Step 4.5 - Graph health check (read-only integrity gate)
-
-A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from pathlib import Path
-from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
-
-extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
-summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
-print(format_diagnostic_report(summary))
-flags = [f'{summary[k]} {label}' for k, label in (
-    ('dangling_endpoint_edges', 'dangling-endpoint edges'),
-    ('missing_endpoint_edges', 'missing-endpoint edges'),
-    ('self_loop_edges', 'self-loop edges'),
-    ('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
-    ('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
-) if summary.get(k, 0)]
-print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
-"
-```
-
-Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
-
-### Step 5 - Label communities
-
-Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
-
-Then regenerate the report and save the labels for the visualizer:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import sys, json
-from graphify.build import build_from_json
-from graphify.cluster import score_all
-from graphify.analyze import god_nodes, surprising_connections, suggest_questions
-from graphify.report import generate
-from pathlib import Path
-
-extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
-detection  = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
-analysis   = json.loads(Path('graphify-out/.graphify_analysis.json').read_text(encoding=\"utf-8\"))
-
-# root= as in Step 4 / the --update runbook (#1361) — same base for node-key parity.
-G = build_from_json(extraction, root='INPUT_PATH', directed=IS_DIRECTED)
-communities = {int(k): v for k, v in analysis['communities'].items()}
-cohesion = {int(k): v for k, v in analysis['cohesion'].items()}
-tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
-
-# LABELS - replace these with the names you chose above
-labels = LABELS_DICT
-
-# Regenerate questions with real community labels (labels affect question phrasing)
-questions = suggest_questions(G, communities, labels)
-
-report = generate(G, communities, cohesion, labels, analysis['gods'], analysis['surprises'], detection, tokens, 'INPUT_PATH', suggested_questions=questions)
-Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
-Path('graphify-out/.graphify_labels.json').write_text(json.dumps({str(k): v for k, v in labels.items()}, ensure_ascii=False), encoding=\"utf-8\")
-print('Report updated with community labels')
-"
-```
-
-Replace `LABELS_DICT` with the actual dict you constructed (e.g. `{0: "Attention Mechanism", 1: "Training Pipeline"}`).
-Replace INPUT_PATH with the actual path.
-
-### Step 6 - Generate Obsidian vault (opt-in) + HTML
-
-**Generate HTML always** (unless `--no-viz`). **Obsidian vault only if `--obsidian` was explicitly given** — skip it otherwise, it generates one file per node.
-
-If `--obsidian` was given:
-
-- If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
-
-```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
-```
-
-Generate the HTML graph (always, unless `--no-viz`):
-
-```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
-```
-
-### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
-
-These run only when their flag is present (`--wiki`, `--neo4j`/`--neo4j-push`, `--falkordb`/`--falkordb-push`, `--svg`, `--graphml`, `--mcp`) or, for the token-reduction benchmark, when `total_words` exceeds 5,000. A default run with no export flags skips all of them. See `references/exports.md` for each one. Run any `--wiki` export before Step 9 cleanup so `.graphify_labels.json` is still available.
-
----
-
-### Step 9 - Save manifest, update cost tracker, clean up, and report
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from pathlib import Path
-from datetime import datetime, timezone
-from graphify.detect import save_manifest
-
-# Save manifest for --update
-detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
-# In --update mode, 'all_files' carries the full corpus; 'files' is the changed
-# subset. Full-rebuild mode populates only 'files', so the fallback handles that.
-# root= relativizes the manifest keys to the scan root (same base as the build),
-# so the on-disk manifest is portable across clones/machines and a later --update
-# matches cached files instead of missing every one (#1417).
-save_manifest(detect.get('all_files') or detect['files'], root='INPUT_PATH')
-
-# Update cumulative cost tracker
-extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
-input_tok = extract.get('input_tokens', 0)
-output_tok = extract.get('output_tokens', 0)
-
-cost_path = Path('graphify-out/cost.json')
-if cost_path.exists():
-    cost = json.loads(cost_path.read_text(encoding=\"utf-8\"))
-else:
-    cost = {'runs': [], 'total_input_tokens': 0, 'total_output_tokens': 0}
-
-cost['runs'].append({
-    'date': datetime.now(timezone.utc).isoformat(),
-    'input_tokens': input_tok,
-    'output_tokens': output_tok,
-    'files': detect.get('total_files', 0),
-})
-cost['total_input_tokens'] += input_tok
-cost['total_output_tokens'] += output_tok
-cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"utf-8\")
-
-print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
-print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
-"
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
-```
-
-Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
-
-Tell the user (omit the obsidian line unless --obsidian was given):
-```
-Graph complete. Outputs in PATH_TO_DIR/graphify-out/
-
-  graph.html            - interactive graph, open in browser
-  GRAPH_REPORT.md       - audit report
-  graph.json            - raw graph data
-  obsidian/             - Obsidian vault (only if --obsidian was given)
-```
-
-If graphify saved you time, consider supporting it: https://github.com/sponsors/safishamsi
-
-Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
-
-Then paste these sections from GRAPH_REPORT.md directly into the chat:
-- God Nodes
-- Surprising Connections
-- Suggested Questions
-
-Do NOT paste the full report - just those three sections. Keep it concise.
-
-Then immediately offer to explore. Pick the single most interesting suggested question from the report - the one that crosses the most community boundaries or has the most surprising bridge node - and ask:
-
-> "The most interesting question this graph can answer: **[question]**. Want me to trace it?"
-
-If the user says yes, run `/graphify query "[question]"` on the graph and walk them through the answer using the graph structure - which nodes connect, which community boundaries get crossed, what the path reveals. Keep going as long as they want to explore. Each answer should end with a natural follow-up ("this connects to X - want to go deeper?") so the session feels like navigation, not a one-shot report.
-
-The graph is the map. Your job after the pipeline is to be the guide.
-
----
-
-## Interpreter guard for subcommands
-
-Before running any subcommand below (`--update`, `--cluster-only`, `query`, `path`, `explain`, `add`), check that `.graphify_python` exists. If it's missing (e.g. user deleted `graphify-out/`), re-resolve the interpreter first:
-
-```bash
-if [ ! -f graphify-out/.graphify_python ]; then
-    GRAPHIFY_BIN=$(which graphify 2>/dev/null)
-    if [ -n "$GRAPHIFY_BIN" ]; then
-        PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
-        case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
-    else
-        PYTHON="python3"
-    fi
-    mkdir -p graphify-out
-    "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
-fi
-```
-
-## For --update and --cluster-only
-
-Both are non-default subcommands. `--update` re-extracts only new or changed files; `--cluster-only` reruns clustering on the existing graph. See `references/update.md` for both flows.
-
----
-
-## For /graphify query
-
-When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
-
-```bash
-graphify query "<question>"
-```
-
-Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.
-
----
-
-## For /graphify add and --watch
-
-Neither is part of the default build. When the user runs `/graphify add <url>` to fetch a URL into the corpus, or passes `--watch` to auto-rebuild on file changes, see `references/add-watch.md`.
-
----
-
-## For the commit hook and native CLAUDE.md integration
-
-When the user asks to install the post-commit auto-rebuild hook or wire graphify into a project's CLAUDE.md, see `references/hooks.md`.
-
----
-
-## Honesty Rules
-
-- Never invent an edge. If unsure, use AMBIGUOUS.
-- Never skip the corpus check warning.
-- Always show token cost in the report.
-- Never hide cohesion scores behind symbols - show the raw number.
-- Never run HTML viz on a graph with more than 5,000 nodes without warning the user.

skills/graphify/references/add-watch.md

@@ -1,56 +0,0 @@
-# graphify reference: add a URL and watch a folder
-
-Load this when the user ran `/graphify add <url>` or passed `--watch`. Neither is part of the default build.
-
-## For /graphify add
-
-Fetch a URL and add it to the corpus, then update the graph.
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import sys
-from graphify.ingest import ingest
-from pathlib import Path
-
-try:
-    out = ingest('URL', Path('./raw'), author='AUTHOR', contributor='CONTRIBUTOR')
-    print(f'Saved to {out}')
-except ValueError as e:
-    print(f'error: {e}', file=sys.stderr)
-    sys.exit(1)
-except RuntimeError as e:
-    print(f'error: {e}', file=sys.stderr)
-    sys.exit(1)
-"
-```
-
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
-
-Supported URL types (auto-detected):
-- YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
-- Twitter/X → fetched via oEmbed, saved as `.md` with tweet text and author
-- arXiv → abstract + metadata saved as `.md`
-- PDF → downloaded as `.pdf`
-- Images (.png/.jpg/.webp) → downloaded, Claude vision extracts on next run
-- Any webpage → converted to markdown via html2text
-
----
-
-## For --watch
-
-Start a background watcher that monitors a folder and auto-updates the graph when files change.
-
-```bash
-$(cat graphify-out/.graphify_python) -m graphify.watch INPUT_PATH --debounce 3
-```
-
-Replace INPUT_PATH with the folder to watch. Behavior depends on what changed:
-
-- **Code files only (.py, .ts, .go, etc.):** re-runs AST extraction + rebuild + cluster immediately, no LLM needed. `graph.json` and `GRAPH_REPORT.md` are updated automatically.
-- **Docs, papers, or images:** writes a `graphify-out/needs_update` flag and prints a notification to run `/graphify --update` (LLM semantic re-extraction required).
-
-Debounce (default 3s): waits until file activity stops before triggering, so a wave of parallel agent writes doesn't trigger a rebuild per file.
-
-Press Ctrl+C to stop.
-
-For agentic workflows: run `--watch` in a background terminal. Code changes from agent waves are picked up automatically between waves. If agents are also writing docs or notes, you'll need a manual `/graphify --update` after those waves.

skills/graphify/references/exports.md

@@ -1,87 +0,0 @@
-# graphify reference: extra exports and benchmark
-
-Load this when the user passed one of the export flags (`--wiki`, `--neo4j`, `--neo4j-push`, `--falkordb`, `--falkordb-push`, `--svg`, `--graphml`, `--mcp`), or when the corpus is large enough for the token-reduction benchmark. Each step runs only for its own flag.
-
-### Step 6b - Wiki (only if --wiki flag)
-
-**Only run this step if `--wiki` was explicitly given in the original command.**
-
-Run this before Step 9 (cleanup) so `.graphify_labels.json` is still available.
-
-```bash
-graphify export wiki
-```
-
-### Step 7 - Neo4j export (only if --neo4j or --neo4j-push flag)
-
-**If `--neo4j`** - generate a Cypher file for manual import:
-
-```bash
-graphify export neo4j
-```
-
-**If `--neo4j-push <uri>`** - push directly to a running Neo4j instance. Ask the user for credentials if not provided:
-
-```bash
-graphify export neo4j --push bolt://localhost:7687 --user neo4j --password PASSWORD
-```
-
-Default URI is `bolt://localhost:7687`, default user is `neo4j`. Uses MERGE - safe to re-run without creating duplicates.
-
-### Step 7a - FalkorDB export (only if --falkordb or --falkordb-push flag)
-
-**If `--falkordb`** - generate a Cypher file. The statements are OpenCypher, but FalkorDB's `GRAPH.QUERY` runs one statement at a time (no bulk script import like Neo4j's `cypher-shell`), so prefer `--falkordb-push` to load a graph. Use this only when you want the portable `cypher.txt` artifact:
-
-```bash
-graphify export falkordb
-```
-
-**If `--falkordb-push <uri>`** - push directly to a running FalkorDB instance. Credentials are optional; ask the user only if the instance requires auth:
-
-```bash
-graphify export falkordb --push falkordb://localhost:6379
-```
-
-Default URI is `falkordb://localhost:6379` (the scheme is informational - `redis://` or a bare `host:port` work too), auth is optional, and the target graph defaults to `graphify`. Uses MERGE - safe to re-run without creating duplicates.
-
-### Step 7b - SVG export (only if --svg flag)
-
-```bash
-graphify export svg
-```
-
-### Step 7c - GraphML export (only if --graphml flag)
-
-```bash
-graphify export graphml
-```
-
-### Step 7d - MCP server (only if --mcp flag)
-
-```bash
-$(cat graphify-out/.graphify_python) -m graphify.serve graphify-out/graph.json
-```
-
-This starts a stdio MCP server that exposes tools: `query_graph`, `get_node`, `get_neighbors`, `get_community`, `god_nodes`, `graph_stats`, `shortest_path`. Add to Claude Desktop or any MCP-compatible agent orchestrator so other agents can query the graph live.
-
-To configure in Claude Desktop, add to `claude_desktop_config.json`. Claude Desktop can't run `$(...)`, and under `uv tool install` the system `python3` can't import graphify — so set `command` to the **absolute interpreter path** printed by `cat graphify-out/.graphify_python`:
-```json
-{
-  "mcpServers": {
-    "graphify": {
-      "command": "<absolute path from: cat graphify-out/.graphify_python>",
-      "args": ["-m", "graphify.serve", "/absolute/path/to/graphify-out/graph.json"]
-    }
-  }
-}
-```
-
-### Step 8 - Token reduction benchmark (only if total_words > 5000)
-
-If `total_words` from `graphify-out/.graphify_detect.json` is greater than 5,000, run:
-
-```bash
-graphify benchmark
-```
-
-Print the output directly in chat. If `total_words <= 5000`, skip silently - the graph value is structural clarity, not token compression, for small corpora.

skills/graphify/references/extraction-spec.md

@@ -1,70 +0,0 @@
-# graphify reference: extraction subagent prompt
-
-Load this in Step 3 Part B when the corpus has at least one doc, paper, or image chunk. A pure-code corpus skips Part B and never reads this file. Each semantic subagent receives the prompt below verbatim (substitute FILE_LIST, CHUNK_NUM, TOTAL_CHUNKS, DEEP_MODE, and CHUNK_PATH).
-
-```
-You are a graphify extraction subagent. Read the files listed and extract a knowledge graph fragment.
-Output ONLY valid JSON matching the schema below - no explanation, no markdown fences, no preamble.
-
-Files (chunk CHUNK_NUM of TOTAL_CHUNKS):
-FILE_LIST
-
-Rules:
-- EXTRACTED: relationship explicit in source (import, call, citation, "see §3.2")
-- INFERRED: reasonable inference (shared data structure, implied dependency)
-- AMBIGUOUS: uncertain - flag for review, do not omit
-
-Code files: focus on semantic edges AST cannot find (call relationships, shared data, arch patterns).
-  Do not re-extract imports - AST already has those.
-Doc/paper files: extract named concepts, entities, citations. For rationale (WHY decisions were made, trade-offs, design intent): store as a `rationale` attribute on the relevant concept node — do NOT create a separate rationale node or fragment node. Only create a node for something that is itself a named entity or concept. Use `file_type:"rationale"` for concept-like nodes (ideas, principles, mechanisms, design patterns). `file_type` MUST be one of exactly these six values: `code`, `document`, `paper`, `image`, `rationale`, `concept`. Any other value is invalid and will be rejected.
-Code files: when adding `calls` edges, source MUST be the caller (the function/class doing the calling), target MUST be the callee. Never reverse this direction. `calls` edges MUST stay within one language: a Python function cannot `calls` a JS/TS/Go/Rust/Java symbol and vice versa — cross-language call edges are phantom artifacts, never emit them.
-Image files: use vision to understand what the image IS - do not just OCR.
-  UI screenshot: layout patterns, design decisions, key elements, purpose.
-  Chart: metric, trend/insight, data source.
-  Tweet/post: claim as node, author, concepts mentioned.
-  Diagram: components and connections.
-  Research figure: what it demonstrates, method, result.
-  Handwritten/whiteboard: ideas and arrows, mark uncertain readings AMBIGUOUS.
-
-DEEP_MODE (if --mode deep was given): be aggressive with INFERRED edges - indirect deps,
-  shared assumptions, latent couplings. Mark uncertain ones AMBIGUOUS instead of omitting.
-
-Semantic similarity: if two concepts in this chunk solve the same problem or represent the same idea without any structural link (no import, no call, no citation), add a `semantically_similar_to` edge marked INFERRED with a confidence_score reflecting how similar they are (0.6-0.95). Examples:
-- Two functions that both validate user input but never call each other
-- A class in code and a concept in a paper that describe the same algorithm
-- Two error types that handle the same failure mode differently
-Only add these when the similarity is genuinely non-obvious and cross-cutting. Do not add them for trivially similar things.
-
-Hyperedges: if 3 or more nodes clearly participate together in a shared concept, flow, or pattern that is not captured by pairwise edges alone, add a hyperedge to a top-level `hyperedges` array. Examples:
-- All classes that implement a common protocol or interface
-- All functions in an authentication flow (even if they don't all call each other)
-- All concepts from a paper section that form one coherent idea
-Use sparingly — only when the group relationship adds information beyond the pairwise edges. Maximum 3 hyperedges per chunk.
-
-If a file has YAML frontmatter (--- ... ---), copy source_url, captured_at, author,
-  contributor onto every node from that file.
-
-confidence_score is REQUIRED on every edge - never omit it, never use 0.5 as a default:
-- EXTRACTED edges: confidence_score = 1.0 always
-- INFERRED edges: pick exactly ONE value from this set — never 0.5:
-    0.95  direct structural evidence (shared data structure, named cross-file reference).
-    0.85  strong inference (clear functional alignment, no direct symbol link).
-    0.75  reasonable inference (shared problem domain + similar shape, requires interpretation).
-    0.65  weak inference (thematically related, no shape evidence).
-    0.55  speculative but plausible (surface-level co-occurrence only).
-  Models follow discrete rubrics better than continuous ranges; the bimodal
-  distribution observed in production (>50% at 0.5, >40% at 0.85+) shows the
-  range guidance is being collapsed to a binary. If no value above fits, mark
-  the edge AMBIGUOUS rather than picking 0.4 or below.
-- AMBIGUOUS edges: 0.1-0.3
-
-Node ID format: lowercase, only `[a-z0-9_]`, no dots or slashes. Format: `{stem}_{entity}` where stem is the **full repo-relative path with the extension dropped**, every path segment kept and joined with `_` (each segment lowercased with non-alphanumeric chars replaced by `_`), and entity is the symbol name similarly normalized. Use every directory level, not just the immediate parent — this keeps same-named files in different directories distinct. Examples: `src/auth/session.py` + `ValidateToken` → `src_auth_session_validatetoken`; `lib/utils/helpers.py` + `parse_url` → `lib_utils_helpers_parse_url`; `tests/test_foo.py` + `_helper` → `tests_test_foo_helper`; `docs/v1/api/README.md` + `getUser` → `docs_v1_api_readme_getuser`. Top-level files (no parent dir, e.g. `setup.py`) use just the filename stem: `setup_my_func`. This must match the ID the AST extractor generates — using just the filename (e.g., `session_validatetoken`) or only the immediate parent (e.g., `auth_session_validatetoken`) will create orphan ghost-duplicate nodes. If you are re-extracting a project built under the old immediate-parent format, the user should run `graphify extract --force` to rebuild cleanly. CRITICAL: never append chunk numbers, sequence numbers, or any suffix to an ID (no `_c1`, `_c2`, `_chunk2`, etc.). IDs must be deterministic from the label alone — the same entity must always produce the same ID regardless of which chunk processes it.
-
-Generate the extraction JSON matching this schema exactly:
-{"nodes":[{"id":"auth_session_validatetoken","label":"Human Readable Name","file_type":"code|document|paper|image|rationale|concept","source_file":"<FILE_LIST path verbatim>","source_location":null,"source_url":null,"captured_at":null,"author":null,"contributor":null}],"edges":[{"source":"node_id","target":"node_id","relation":"calls|implements|references|cites|conceptually_related_to|shares_data_with|semantically_similar_to|rationale_for","confidence":"EXTRACTED|INFERRED|AMBIGUOUS","confidence_score":1.0,"source_file":"<FILE_LIST path verbatim>","source_location":null,"weight":1.0}],"hyperedges":[{"id":"snake_case_id","label":"Human Readable Label","nodes":["node_id1","node_id2","node_id3"],"relation":"participate_in|implement|form","confidence":"EXTRACTED|INFERRED","confidence_score":0.75,"source_file":"<FILE_LIST path verbatim>"}],"input_tokens":0,"output_tokens":0}
-
-source_file RULE (every node, edge, and hyperedge): set source_file to the path of the originating file EXACTLY as it appears in FILE_LIST — verbatim and absolute. Do NOT shorten to a basename, do NOT re-relativize, do NOT strip any directory prefix, and do NOT change separators (the engine canonicalizes separators and relativizes against the build root downstream). Copy the FILE_LIST entry character-for-character. This keeps the full build and incremental --update on the same base, so build_merge's replace-on-re-extract matches the existing node instead of accumulating a duplicate.
-
-Then write the JSON to disk using the Write tool at this exact absolute path (no relative paths — Write resolves relative paths against an undefined cwd and the file will be silently lost):
-CHUNK_PATH
-```

skills/graphify/references/github-and-merge.md

@@ -1,46 +0,0 @@
-# graphify reference: GitHub clone and cross-repo merge
-
-Load this when the user passed one or more `https://github.com/...` URLs, or named several local subfolders to merge into one graph.
-
-### Step 0 - Clone GitHub repo(s) (only if a GitHub URL was given)
-
-**Single repo:**
-```bash
-LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
-# Use LOCAL_PATH as the target for all subsequent steps
-```
-
-**Multiple repos (cross-repo graph):**
-```bash
-# Clone each repo, run the full pipeline on each, then merge
-graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
-graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
-# Run /graphify on each local path to produce their graph.json files
-# Then merge:
-graphify merge-graphs \
-  ~/.graphify/repos/<owner1>/<repo1>/graphify-out/graph.json \
-  ~/.graphify/repos/<owner2>/<repo2>/graphify-out/graph.json \
-  --out graphify-out/cross-repo-graph.json
-```
-
-Graphify clones into `~/.graphify/repos/<owner>/<repo>` and reuses existing clones on repeat runs. Each node in the merged graph carries a `repo` attribute so you can filter by origin.
-
-**Multiple local subfolders (monorepo or multi-service layout):**
-
-The skill pipeline writes all intermediate and final outputs to `graphify-out/` in the current working directory. Running the skill on each subfolder separately will clobber the same output dir. Instead, use the CLI directly for each subfolder — it places `graphify-out/` *inside* the scanned path:
-
-```bash
-graphify extract ./core/     # → ./core/graphify-out/graph.json
-graphify extract ./service/  # → ./service/graphify-out/graph.json
-graphify extract ./platform/ # → ./platform/graphify-out/graph.json
-# Add --backend gemini|kimi|openai|deepseek|claude-cli depending on which API key you have set
-
-# Then merge at the project root:
-graphify merge-graphs \
-  ./core/graphify-out/graph.json \
-  ./service/graphify-out/graph.json \
-  ./platform/graphify-out/graph.json \
-  --out graphify-out/graph.json
-```
-
-Once `graphify-out/graph.json` exists, the fast path above takes over: any codebase question runs `graphify query` directly on the merged graph — no re-extraction, no size gate.

skills/graphify/references/hooks.md

@@ -1,33 +0,0 @@
-# graphify reference: commit hook and native CLAUDE.md integration
-
-Load this when the user asked to install the post-commit hook or wire graphify into a project's CLAUDE.md.
-
-## For git commit hook
-
-Install a post-commit hook that auto-rebuilds the graph after every commit. No background process needed - triggers once per commit, works with any editor.
-
-```bash
-graphify hook install    # install
-graphify hook uninstall  # remove
-graphify hook status     # check
-```
-
-After every `git commit`, the hook detects which code files changed (via `git diff HEAD~1`), re-runs AST extraction on those files, and rebuilds `graph.json` and `GRAPH_REPORT.md`. Doc/image changes are ignored by the hook - run `/graphify --update` manually for those.
-
-If a post-commit hook already exists, graphify appends to it rather than replacing it.
-
----
-
-## For native CLAUDE.md integration
-
-Run once per project to make graphify always-on in Claude Code sessions:
-
-```bash
-graphify claude install
-```
-
-This writes a `## graphify` section to the local `CLAUDE.md` that instructs Claude to check the graph before answering codebase questions and rebuild it after code changes. No manual `/graphify` needed in future sessions.
-
-```bash
-graphify claude uninstall  # remove the section
-```

skills/graphify/references/query.md

@@ -1,311 +0,0 @@
-# graphify reference: query, path, explain
-
-Load this when the user asks a question against an existing graph, or runs `/graphify path` or `/graphify explain`. The core's query stub points here for the full traversal flow. These flows use the `graphify query` CLI when it is available and fall back to an inline NetworkX traversal otherwise.
-
-Two traversal modes - choose based on the question:
-
-| Mode | Flag | Best for |
-|------|------|----------|
-| BFS (default) | _(none)_ | "What is X connected to?" - broad context, nearest neighbors first |
-| DFS | `--dfs` | "How does X reach Y?" - trace a specific chain or dependency path |
-
-First check the graph exists:
-```bash
-$(cat graphify-out/.graphify_python) -c "
-from pathlib import Path
-if not Path('graphify-out/graph.json').exists():
-    print('ERROR: No graph found. Run /graphify <path> first to build the graph.')
-    raise SystemExit(1)
-"
-```
-If it fails, stop and tell the user to run `/graphify <path>` first.
-
-### Step 0 — Constrained query expansion (REQUIRED before traversal)
-
-graphify's `query` CLI matches nodes via case-folded substring + IDF — there is **no stemming, no synonyms, no cross-language match** inside the binary, and the inline fallback below matches the same way. If the user's question uses different language or different domain vocabulary than the graph's labels (user says "обработчик" / graph says "handler"; user says "authentication" / graph says "Guardian"), the literal matcher returns 0 hits and the answer collapses to noise.
-
-Fix this **without inventing tokens** by expanding the query against the actual graph vocabulary first:
-
-1. Extract the token vocabulary from node labels:
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json, re
-from pathlib import Path
-data = json.loads(Path('graphify-out/graph.json').read_text(encoding='utf-8'))
-vocab = set()
-for n in data['nodes']:
-    for c in re.findall(r'[^\W\d_]+', n.get('label','') or '', re.UNICODE):
-        parts = re.findall(r'[A-Z]+(?=[A-Z][a-z])|[A-Z]?[a-z]+|[A-Z]+', c) or [c]
-        for p in parts:
-            t = p.lower()
-            if 3 <= len(t) <= 30:
-                vocab.add(t)
-Path('graphify-out/.vocab.txt').write_text('\n'.join(sorted(vocab)), encoding='utf-8')
-print(f'vocab: {len(vocab)} tokens')
-"
-```
-
-2. Read `graphify-out/.vocab.txt`. Then for the user's question, select **up to 12 tokens from this exact list** that semantically match the query intent. Hard constraints:
-   - You MUST pick only tokens present in the vocabulary file. Do NOT invent tokens.
-   - If a query concept has no plausible token in the vocab, skip it — do not substitute a near-synonym from training memory.
-   - If **no** vocab tokens match the query at all, output an empty list and tell the user the corpus has no relevant vocabulary for this question. Do not fabricate a search.
-   - Translate cross-language: Russian "аутентификация" → look for `auth`, `credential`, `token`, `security` IFF present in vocab.
-   - Morphology: "handlers" maps to `handler` IFF present; "todos" maps to `todo` IFF present.
-
-3. Print the selection explicitly to the user before running the query, so the expansion is auditable:
-```
-Query expanded to (from graph vocab, N tokens): [token1, token2, ...]
-```
-If the list is empty, say so plainly and stop — do not proceed to traversal.
-
-### Step 1 — Traversal
-
-Build the **expanded query string** by joining the selected tokens with spaces. Use this string as `QUESTION` below — NOT the original user question. (The original question is preserved only for `save-result` at the end.)
-
-Prefer the CLI when it is installed:
-```bash
-graphify query "QUESTION"
-# or: graphify query "QUESTION" --dfs --budget 3000
-```
-
-If the CLI is unavailable, load `graphify-out/graph.json` and run the traversal inline:
-
-1. Find the 1-3 nodes whose label best matches the expanded tokens.
-2. Run the appropriate traversal from each starting node.
-3. Read the subgraph - node labels, edge relations, confidence tags, source locations.
-4. Answer using **only** what the graph contains. Quote `source_location` when citing a specific fact.
-5. If the graph lacks enough information, say so - do not hallucinate edges.
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import sys, json
-from networkx.readwrite import json_graph
-import networkx as nx
-from pathlib import Path
-
-data = json.loads(Path('graphify-out/graph.json').read_text(encoding='utf-8'))
-G = json_graph.node_link_graph(data, edges='links')
-
-question = 'QUESTION'
-mode = 'MODE'  # 'bfs' or 'dfs'
-terms = [t.lower() for t in question.split() if len(t) >= 3]  # match the vocab threshold; keeps api/jwt/ios (#1392)
-
-# Find best-matching start nodes
-scored = []
-for nid, ndata in G.nodes(data=True):
-    label = ndata.get('label', '').lower()
-    score = sum(1 for t in terms if t in label)
-    if score > 0:
-        scored.append((score, nid))
-scored.sort(reverse=True)
-start_nodes = [nid for _, nid in scored[:3]]
-
-if not start_nodes:
-    print('No matching nodes found for query terms:', terms)
-    sys.exit(0)
-
-subgraph_nodes = set()
-subgraph_edges = []
-
-if mode == 'dfs':
-    # DFS: follow one path as deep as possible before backtracking.
-    # Depth-limited to 6 to avoid traversing the whole graph.
-    visited = set()
-    stack = [(n, 0) for n in reversed(start_nodes)]
-    while stack:
-        node, depth = stack.pop()
-        if node in visited or depth > 6:
-            continue
-        visited.add(node)
-        subgraph_nodes.add(node)
-        for neighbor in G.neighbors(node):
-            if neighbor not in visited:
-                stack.append((neighbor, depth + 1))
-                subgraph_edges.append((node, neighbor))
-else:
-    # BFS: explore all neighbors layer by layer up to depth 3.
-    frontier = set(start_nodes)
-    subgraph_nodes = set(start_nodes)
-    for _ in range(3):
-        next_frontier = set()
-        for n in frontier:
-            for neighbor in G.neighbors(n):
-                if neighbor not in subgraph_nodes:
-                    next_frontier.add(neighbor)
-                    subgraph_edges.append((n, neighbor))
-        subgraph_nodes.update(next_frontier)
-        frontier = next_frontier
-
-# Token-budget aware output: rank by relevance, cut at budget (~4 chars/token)
-token_budget = BUDGET  # default 2000
-char_budget = token_budget * 4
-
-# Score each node by term overlap for ranked output
-def relevance(nid):
-    label = G.nodes[nid].get('label', '').lower()
-    return sum(1 for t in terms if t in label)
-
-ranked_nodes = sorted(subgraph_nodes, key=relevance, reverse=True)
-
-lines = [f'Traversal: {mode.upper()} | Start: {[G.nodes[n].get(\"label\",n) for n in start_nodes]} | {len(subgraph_nodes)} nodes']
-for nid in ranked_nodes:
-    d = G.nodes[nid]
-    lines.append(f'  NODE {d.get(\"label\", nid)} [src={d.get(\"source_file\",\"\")} loc={d.get(\"source_location\",\"\")}]')
-for u, v in subgraph_edges:
-    if u in subgraph_nodes and v in subgraph_nodes:
-        _raw = G[u][v]; d = next(iter(_raw.values()), {}) if isinstance(G, nx.MultiGraph) else _raw
-        lines.append(f'  EDGE {G.nodes[u].get(\"label\",u)} --{d.get(\"relation\",\"\")} [{d.get(\"confidence\",\"\")}]--> {G.nodes[v].get(\"label\",v)}')
-
-output = '\n'.join(lines)
-if len(output) > char_budget:
-    output = output[:char_budget] + f'\n... (truncated at ~{token_budget} token budget - use --budget N for more)'
-print(output)
-"
-```
-
-Replace `QUESTION` with the **expanded** query string, `MODE` with `bfs` or `dfs`, and `BUDGET` with the token budget (default `2000`, or whatever `--budget N` specifies). Then answer based on the subgraph output above, using only what the graph contains.
-
-After writing the answer, save it back into the graph so it improves future queries. Include the expanded tokens inside the `--answer` text (e.g. `"Expanded from original query via vocab: [tokens]. Then traversed..."`) so the next `--update` extracts the expansion history as a graph node:
-
-```bash
-$(cat graphify-out/.graphify_python) -m graphify save-result --question "ORIGINAL_QUESTION" --answer "ANSWER" --type query --nodes NODE1 NODE2
-```
-
-Replace `ORIGINAL_QUESTION` with the user's verbatim question, `ANSWER` with your full answer text (containing the expanded-token trace), `NODE1 NODE2` with the list of node labels you cited. This closes the feedback loop: the next `--update` will extract this Q&A as a node in the graph.
-
-**Work memory (self-improving loop).** Add an `--outcome` so future sessions learn from this one — append `--outcome useful|dead_end|corrected` to the `save-result` command (and `--correction "the right answer"` when correcting):
-
-- `useful` — the cited nodes answered the question well (they become *preferred sources*).
-- `dead_end` — the question/path led nowhere; don't re-derive it next time.
-- `corrected` — the saved answer was wrong; `--correction` records what was right.
-
-At the **start** of graph work, refresh and read the lessons: run `graphify reflect --if-stale` (cheap, deterministic, no LLM; `--if-stale` makes it a no-op when `LESSONS.md` is already newer than every input, e.g. when the git hook just refreshed it), then read `graphify-out/reflections/LESSONS.md`. It lists **preferred sources** (start there), **known dead ends** (skip them), and prior **corrections**. Running `reflect` yourself keeps the lessons current even without the git hook installed; if the post-commit hook *is* installed, `--if-stale` means your session-start run costs almost nothing.
-
----
-
-## For /graphify path
-
-Find the shortest path between two named concepts in the graph. Prefer the CLI when installed:
-
-```bash
-graphify path "NODE_A" "NODE_B"
-```
-
-If the CLI is unavailable, run it inline:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json, sys
-import networkx as nx
-from networkx.readwrite import json_graph
-from pathlib import Path
-
-data = json.loads(Path('graphify-out/graph.json').read_text(encoding='utf-8'))
-G = json_graph.node_link_graph(data, edges='links')
-
-a_term = 'NODE_A'
-b_term = 'NODE_B'
-
-def find_node(term):
-    term = term.lower()
-    scored = sorted(
-        [(sum(1 for w in term.split() if w in G.nodes[n].get('label','').lower()), n)
-         for n in G.nodes()],
-        reverse=True
-    )
-    return scored[0][1] if scored and scored[0][0] > 0 else None
-
-src = find_node(a_term)
-tgt = find_node(b_term)
-
-if not src or not tgt:
-    print(f'Could not find nodes matching: {a_term!r} or {b_term!r}')
-    sys.exit(0)
-
-try:
-    path = nx.shortest_path(G, src, tgt)
-    print(f'Shortest path ({len(path)-1} hops):')
-    for i, nid in enumerate(path):
-        label = G.nodes[nid].get('label', nid)
-        if i < len(path) - 1:
-            _raw = G[nid][path[i+1]]; edge = next(iter(_raw.values()), {}) if isinstance(G, nx.MultiGraph) else _raw
-            rel = edge.get('relation', '')
-            conf = edge.get('confidence', '')
-            print(f'  {label} --{rel}--> [{conf}]')
-        else:
-            print(f'  {label}')
-except nx.NetworkXNoPath:
-    print(f'No path found between {a_term!r} and {b_term!r}')
-except nx.NodeNotFound as e:
-    print(f'Node not found: {e}')
-"
-```
-
-Replace `NODE_A` and `NODE_B` with the actual concept names from the user. Then explain the path in plain language - what each hop means, why it's significant.
-
-After writing the explanation, save it back:
-
-```bash
-$(cat graphify-out/.graphify_python) -m graphify save-result --question "Path from NODE_A to NODE_B" --answer "ANSWER" --type path_query --nodes NODE_A NODE_B
-```
-
----
-
-## For /graphify explain
-
-Give a plain-language explanation of a single node - everything connected to it. Prefer the CLI when installed:
-
-```bash
-graphify explain "NODE_NAME"
-```
-
-If the CLI is unavailable, run it inline:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json, sys
-import networkx as nx
-from networkx.readwrite import json_graph
-from pathlib import Path
-
-data = json.loads(Path('graphify-out/graph.json').read_text(encoding='utf-8'))
-G = json_graph.node_link_graph(data, edges='links')
-
-term = 'NODE_NAME'
-term_lower = term.lower()
-
-# Find best matching node
-scored = sorted(
-    [(sum(1 for w in term_lower.split() if w in G.nodes[n].get('label','').lower()), n)
-     for n in G.nodes()],
-    reverse=True
-)
-if not scored or scored[0][0] == 0:
-    print(f'No node matching {term!r}')
-    sys.exit(0)
-
-nid = scored[0][1]
-data_n = G.nodes[nid]
-print(f'NODE: {data_n.get(\"label\", nid)}')
-print(f'  source: {data_n.get(\"source_file\",\"unknown\")}')
-print(f'  type: {data_n.get(\"file_type\",\"unknown\")}')
-print(f'  degree: {G.degree(nid)}')
-print()
-print('CONNECTIONS:')
-for neighbor in G.neighbors(nid):
-    _raw = G[nid][neighbor]; edge = next(iter(_raw.values()), {}) if isinstance(G, nx.MultiGraph) else _raw
-    nlabel = G.nodes[neighbor].get('label', neighbor)
-    rel = edge.get('relation', '')
-    conf = edge.get('confidence', '')
-    src_file = G.nodes[neighbor].get('source_file', '')
-    print(f'  --{rel}--> {nlabel} [{conf}] ({src_file})')
-"
-```
-
-Replace `NODE_NAME` with the concept the user asked about. Then write a 3-5 sentence explanation of what this node is, what it connects to, and why those connections are significant. Use the source locations as citations.
-
-After writing the explanation, save it back:
-
-```bash
-$(cat graphify-out/.graphify_python) -m graphify save-result --question "Explain NODE_NAME" --answer "ANSWER" --type explain --nodes NODE_NAME
-```

skills/graphify/references/transcribe.md

@@ -1,52 +0,0 @@
-# graphify reference: transcribe video and audio
-
-Load this only when `detect` reported one or more `video` files. A corpus with no video never reads this.
-
-### Step 2.5 - Transcribe video / audio files (only if video files detected)
-
-Skip this step entirely if `detect` returned zero `video` files.
-
-Video and audio files cannot be read directly. Transcribe them to text first, then treat the transcripts as doc files in Step 3.
-
-**Strategy:** Read the god nodes from `graphify-out/.graphify_detect.json` (or the analysis file if it exists from a previous run). You are already a language model — write a one-sentence domain hint yourself from those labels. Then pass it to Whisper as the initial prompt. No separate API call needed.
-
-**However**, if the corpus has *only* video files and no other docs/code, use the generic fallback prompt: `"Use proper punctuation and paragraph breaks."`
-
-**Step 1 - Write the Whisper prompt yourself.**
-
-Read the top god node labels from detect output or analysis, then compose a short domain hint sentence, for example:
-
-- Labels: `transformer, attention, encoder, decoder` → `"Machine learning research on transformer architectures and attention mechanisms. Use proper punctuation and paragraph breaks."`
-- Labels: `kubernetes, deployment, pod, helm` → `"DevOps discussion about Kubernetes deployments and Helm charts. Use proper punctuation and paragraph breaks."`
-
-**Export** it as `GRAPHIFY_WHISPER_PROMPT` (the exact name the transcriber reads — and it must be `export`ed so the child Python process sees it) for the next command.
-
-**Step 2 - Transcribe:**
-
-```bash
-export GRAPHIFY_WHISPER_MODEL=base  # or whatever --whisper-model the user passed (must be exported)
-export GRAPHIFY_WHISPER_PROMPT="<the one-sentence domain hint you composed in Step 1>"
-$(cat graphify-out/.graphify_python) -c "
-import json, os, sys
-from pathlib import Path
-from graphify.transcribe import transcribe_all
-
-detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
-video_files = detect.get('files', {}).get('video', [])
-prompt = os.environ.get('GRAPHIFY_WHISPER_PROMPT', 'Use proper punctuation and paragraph breaks.')
-
-transcript_paths = transcribe_all(video_files, initial_prompt=prompt)
-# Write the JSON from Python (NOT a shell '>' redirect): transcribe_all/Whisper
-# print progress to stdout, which would otherwise corrupt the JSON file (#1392).
-Path('graphify-out/.graphify_transcripts.json').write_text(json.dumps(transcript_paths, ensure_ascii=False), encoding=\"utf-8\")
-print(f'Transcribed {len(transcript_paths)} file(s)', file=sys.stderr)
-"
-```
-
-After transcription:
-- Read the transcript paths from `graphify-out/.graphify_transcripts.json`
-- Add them to the docs list before dispatching semantic subagents in Step 3B
-- Print how many transcripts were created: `Transcribed N video file(s) -> treating as docs`
-- If transcription fails for a file, print a warning and continue with the rest
-
-**Whisper model:** Default is `base`. If the user passed `--whisper-model <name>`, `export GRAPHIFY_WHISPER_MODEL=<name>` (it must be exported, not just assigned) before running the command above.

skills/graphify/references/update.md

@@ -1,192 +0,0 @@
-# graphify reference: incremental update and cluster-only
-
-Load this only when the user passed `--update` or `--cluster-only`. A first-time full build never reads this file.
-
-## For --update (incremental re-extraction)
-
-Use when you've added or modified files since the last run. Only re-extracts changed files - saves tokens and time.
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import sys, json
-from graphify.detect import detect_incremental, save_manifest
-from pathlib import Path
-
-result = detect_incremental(Path('INPUT_PATH'))
-new_total = result.get('new_total', 0)
-print(json.dumps(result, indent=2, ensure_ascii=False))
-Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")
-deleted = list(result.get('deleted_files', []))
-if new_total == 0 and not deleted:
-    print('No files changed since last run. Nothing to update.')
-    raise SystemExit(0)
-if deleted:
-    print(f'{len(deleted)} deleted file(s) to prune.')
-if new_total > 0:
-    print(f'{new_total} new/changed file(s) to re-extract.')
-"
-```
-
-Then populate `.graphify_detect.json` so Steps 3A–6 (which read it unconditionally) see the right state for an incremental run. `files` carries the changed subset (drives Step 3A AST + Step 3B0 cache check on only what changed); `all_files` carries the full corpus for any step that needs corpus-wide context:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from pathlib import Path
-r = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
-Path('graphify-out/.graphify_detect.json').write_text(json.dumps({
-    'files': r.get('new_files', {}),
-    'all_files': r.get('files', {}),
-    'total_files': r.get('new_total', 0),
-    'total_words': r.get('total_words', 0),
-    'skipped_sensitive': r.get('skipped_sensitive', []),
-    'needs_graph': True,
-}, ensure_ascii=False), encoding=\"utf-8\")
-"
-```
-
-If new files exist, first check whether all changed files are code files:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from pathlib import Path
-
-result = json.loads(open('graphify-out/.graphify_incremental.json', encoding='utf-8').read()) if Path('graphify-out/.graphify_incremental.json').exists() else {}
-code_exts = {'.py','.ts','.js','.go','.rs','.java','.cpp','.c','.rb','.swift','.kt','.cs','.scala','.php','.cc','.cxx','.hpp','.h','.kts','.lua','.toc','.f','.F','.f90','.F90','.f95','.F95','.f03','.F03','.f08','.F08'}
-new_files = result.get('new_files', {})
-all_changed = [f for files in new_files.values() for f in files]
-code_only = all(Path(f).suffix.lower() in code_exts for f in all_changed)
-print('code_only:', code_only)
-"
-```
-
-If `code_only` is True: print `[graphify update] Code-only changes detected - skipping semantic extraction (no LLM needed)`, run only Step 3A (AST) on the changed files, skip Step 3B entirely (no subagents), then go straight to merge and Steps 4–8.
-
-If `code_only` is False (any changed file is a doc/paper/image/video): **first, if any changed file is in `new_files['video']`, run `references/transcribe.md` (Step 2.5) on those files, then rewrite `.graphify_detect.json` to move the resulting transcript paths into `files['document']` and drop `files['video']`** — otherwise raw `.mp4/.mp3` paths are fed to semantic subagents as unreadable media (#1392). Then run the full Steps 3A–3C pipeline as normal.
-
-
-If no new files exist (only deletions), create an empty extraction so the merge step can prune:
-
-```bash
-if [ ! -f graphify-out/.graphify_extract.json ]; then
-    echo '[graphify update] Only deletions -- creating empty extraction for merge.'
-    $(cat graphify-out/.graphify_python) -c "
-import json
-from pathlib import Path
-Path('graphify-out/.graphify_extract.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
-"
-fi
-```
-
-
-Then:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from pathlib import Path
-from graphify.build import build_merge
-from graphify.detect import save_manifest
-
-# Load new extraction and incremental state
-new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
-incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
-deleted = list(incremental.get('deleted_files', []))
-# prune_sources is ONLY for genuinely DELETED files. Changed/re-extracted files are
-# handled by build_merge's replace-on-re-extract (#1344): every source_file in
-# new_chunks is dropped from the base before merge, so old/stale nodes don't survive.
-# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
-# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
-# now that replace — not the dedup pass — reconciles changed files).
-prune = list(deleted) or None
-
-# Use build_merge() — reads graph.json directly without NetworkX round-trip
-# so edge direction (calls, implements, imports) is always preserved (#801).
-# Pass root= so prune_sources (absolute paths from detect_incremental) are
-# relativized to match the graph's relative source_file values; without it
-# nothing is pruned and stale nodes accumulate on every update (#1361).
-# directed=IS_DIRECTED: replace IS_DIRECTED with True if --directed was given, else
-# False. Without it a --directed --update silently rebuilds undirected and collapses
-# reciprocal A<->B edges (#1392).
-G = build_merge(
-    [new_extraction],
-    graph_path='graphify-out/graph.json',
-    prune_sources=prune,
-    root='INPUT_PATH',
-    directed=IS_DIRECTED,
-)
-print(f'[graphify update] Merged: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges')
-
-# Write merged result back to .graphify_extract.json so Step 4 sees the full graph
-merged_out = {
-    'nodes': [{'id': n, **d} for n, d in G.nodes(data=True)],
-    'edges': [
-        # Explicit source/target last so they win over any stale attrs in d.
-        {**{k: val for k, val in d.items() if k not in ('_src', '_tgt', 'source', 'target')},
-         'source': d.get('_src', u), 'target': d.get('_tgt', v)}
-        for u, v, d in G.edges(data=True)
-    ],
-    # G.graph["hyperedges"] holds hyperedges from both existing graph.json
-    # and new_extraction (build_merge combines them). Falling back to
-    # new_extraction only would silently drop prior-run hyperedges (#801).
-    'hyperedges': list(G.graph.get('hyperedges', [])),
-    'input_tokens': new_extraction.get('input_tokens', 0),
-    'output_tokens': new_extraction.get('output_tokens', 0),
-}
-Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged_out, ensure_ascii=False), encoding=\"utf-8\")
-print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])} nodes, {len(merged_out[\"edges\"])} edges)')
-
-# Save manifest so next --update diffs against today's state, not the
-# prior run's baseline (prevents ghost-node reports on subsequent updates).
-# root= matches the build_merge call above so the manifest keys stay relative to
-# the scan root — portable across clones/machines, so --update keeps matching
-# cached files instead of missing every one after a move (#1417).
-save_manifest(incremental['files'], root='INPUT_PATH')
-print('[graphify update] Manifest saved.')
-"
-```
-
-Then run Steps 4–8 on the merged graph as normal.
-
-After Step 4, show the graph diff:
-
-```bash
-$(cat graphify-out/.graphify_python) -c "
-import json
-from graphify.analyze import graph_diff
-from graphify.build import build_from_json
-from networkx.readwrite import json_graph
-import networkx as nx
-from pathlib import Path
-
-# Load old graph (before update) from backup written before merge
-old_data = json.loads(Path('graphify-out/.graphify_old.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_old.json').exists() else None
-new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
-G_new = build_from_json(new_extract, directed=IS_DIRECTED)
-
-if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
-    diff = graph_diff(G_old, G_new)
-    print(diff['summary'])
-    if diff['new_nodes']:
-        print('New nodes:', ', '.join(n['label'] for n in diff['new_nodes'][:5]))
-    if diff['new_edges']:
-        print('New edges:', len(diff['new_edges']))
-"
-```
-
-Before the merge step, save the old graph: `cp graphify-out/graph.json graphify-out/.graphify_old.json`
-Clean up after: `rm -f graphify-out/.graphify_old.json`
-
----
-
-## For --cluster-only
-
-Skip Steps 1–3. Re-run clustering on the existing graph:
-
-```bash
-graphify cluster-only .
-```
-
-`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.

templates/settings/SETTINGS.md

@@ -46,6 +46,66 @@ Always write the file-write ban as `Edit(...)`.
 | `auto` | Research preview — agentic default, permission model evolving. This config's default (BDR-004) | Daily driving with guardrails |
 | `bypassPermissions` | Skips all prompts — **dangerous** | CI/CD only, sandboxed env |
 
+## Auto mode (`autoMode`)
+
+With `defaultMode: auto`, a classifier decides each action instead of a static
+prompt. The `autoMode` block is what you hand that classifier.
+
+| Key | What it holds |
+|---|---|
+| `environment` | Facts about the machine and the repo. Context, not rules. |
+| `allow` | Action classes the classifier may clear on its own. |
+| `soft_deny` | Destructive or irreversible actions. Explicit user intent clears them. |
+| `hard_deny` | Security boundaries. User intent does **not** clear them. |
+| `classifyAllShell` | `true` suspends every Bash allow rule so all shell goes through the classifier. |
+
+All four lists are prose spliced into the classifier prompt, not permission-rule
+syntax. Write `Sending SIGKILL reaches processes outside this session`, not
+`Bash(kill -9 *)`.
+
+### `$defaults`
+
+Each list **replaces** the built-in entries unless it contains the literal
+string `"$defaults"`, which splices them in at that position. Put it first and
+your own entries refine what follows. Omit it and you silently drop every
+built-in rule, which is almost never the intent.
+
+### Scope it right
+
+`autoMode` in `~/.claude/settings.json` reaches **every** project on the
+machine. Project facts (this repo's deploy target, its secrets, its data)
+belong in that project's `.claude/settings.local.json`. A global block naming
+one repo feeds the classifier false facts in all the others.
+
+### `ask` is not a prompt under auto mode
+
+Verified in-session (LRN-146): with `defaultMode: auto`, Bash rules in
+`permissions.ask` were auto-approved and raised no prompt. `deny` is the only
+tier the classifier cannot lift.
+
+So for a destructive command you want gated but still reachable, `ask` is the
+wrong tier. Use `autoMode.soft_deny`: blocked until the user's intent clears
+it. Keep `deny` for what must never run at all.
+
+### Picking a tier
+
+| You want | Tier |
+|---|---|
+| Never runs, no exception, matchable by a command pattern | `permissions.deny` |
+| Never runs, and a pattern cannot express it (a read then a send, a prod target) | `autoMode.hard_deny` |
+| Runs when the user asks for it, blocked otherwise | `autoMode.soft_deny` |
+| Runs freely | `permissions.allow`, or nothing |
+
+`permissions.ask` is not on this list on purpose. Under `defaultMode: auto` it
+gates nothing.
+
+### Scope of intent
+
+A `soft_deny` clears on the user's instruction, and this config scopes that to
+the **current turn**. An approval from an earlier turn is not an approval now.
+State the scope in the rules themselves: the classifier reads the list, it has
+no separate setting for this.
+
 ## Security notes
 
 - `Read(**/.env)` only blocks the Read tool. `Bash(cat .env)` bypasses it unless separately denied.
@@ -53,6 +113,8 @@ Always write the file-write ban as `Edit(...)`.
 - `disableBypassPermissionsMode: "disable"` prevents switching to bypass mode mid-session.
 - Prefer `ask` over `allow` for anything touching external systems.
 - `deny` in `~/.claude/settings.json` cannot be overridden by project-level `allow` — deny always wins.
+- Under `defaultMode: auto`, `ask` does not raise a prompt (see above). A destructive
+  command belongs in `deny` or in `autoMode.soft_deny`, not in `ask`.
 
 ## managed-settings.json (enterprise)
 

update-all.sh

@@ -15,8 +15,10 @@ REPO="$(cd "$(dirname "$0")" && pwd)"
 VERSION=$(cat "$REPO/version.txt" 2>/dev/null || echo "unknown")
 
 # Load shared detection library
-# shellcheck source=lib/detect-plugins.sh
+# shellcheck source=lib/detect-plugins.sh disable=SC1091
 source "$REPO/lib/detect-plugins.sh"
+# shellcheck source=lib/gstack-playwright.sh disable=SC1091
+source "$REPO/lib/gstack-playwright.sh"
 
 echo ""
 echo "═══ claude-config update (v${VERSION}) ═══"
@@ -84,7 +86,7 @@ if [[ "$_gstack_confirm" =~ ^[Yy]$ ]]; then
     _gstack_state=$(bash "$REPO/lib/toggle-external.sh" status gstack 2>/dev/null || echo "unknown")
   fi
 
-  if git submodule update --remote skills-external/gstack 2>/dev/null; then
+  if gstack_submodule_update_with_bump "$REPO"; then
     if [ -d "skills-external/gstack" ]; then
       if [ -x "skills-external/gstack/setup" ]; then
         if (cd skills-external/gstack && ./setup) 2>/dev/null; then