job6: capitalize — BDR-056, LRN-107, EVAL-020, journal

BDR-056: deps policy reversal — latest gated by integration, not
KEEP-PINNED by default (job6-batch-3 override, gstack #1911 case).
LRN-107: read-only subagent mandates must ban copying secret VALUES,
not just mutations (job6's own MAGIC_API_KEY scratch-copy incident).
EVAL-020: job6 execution quality — 2 real STOP gates hit and resolved
live (graphifyy hook rewrite declined, gsd-pi format break patched).

.claude/memory/decisions.md

@@ -76,6 +76,7 @@ rules:
 | BDR-052 | 2026-07-05 | /tour auto mode = branch-as-gate: no mid-run approval gates; unmerged chore branch + per-project TOUR.md = deferred human gate; reconcile report-only; loop bounded 3× | accepted |
 | BDR-054 | 2026-07-06 | supersede BDR-038 NEXT.sh/hand-back artifacts — shipped impl removed both (52f6678, LRN-102) | accepted |
 | BDR-055 | 2026-07-07 | job5: delete memory-commit/doc-commit `pending` verbs — v2 hook rejected (BDR-037), J4-17 closed MOOT | accepted |
+| BDR-056 | 2026-07-07 | job6: deps policy = latest gated by integration, not KEEP-PINNED by default | accepted |
 
 ---
 
@@ -862,3 +863,15 @@ rules:
 - **Why**: headers earmarked both funcs "for the v2 hook" — [[BDR-037]] REJECTED v2 hook, no code ever written. J4-17 queued TEST not DELETE, but deferred to the newer/wrong branch — v2 hook dead means nothing left to test toward. Zero prod/test callers confirmed (job5 audit) before delete.
 - **Alternatives rejected**: keep+test per J4-17 (tests a dead-end, [[BDR-037]] already closed that door); keep unused (dead code, no consumer).
 - **Reference**: commit `da3abf9`; `.audit/job5-report.md` J5-13/§3b; supersedes J4-17 (`.audit/job4-report.md:35`). Same supersession-trace discipline [[BDR-054]] had to backfill for BDR-038/job3 D6-D9 — written here at delete time, not reconstructed later.
+
+---
+
+## BDR-056 — job6: deps policy = latest gated by integration, not KEEP-PINNED by default
+
+- **Date**: 2026-07-07
+- **Status**: accepted (reverses job6-batch-3 KEEP-PINNED-unless-CVE default)
+- **Decision**: default posture = pull latest, gated per-dep by real integration checks (make test + named smoke), not "keep pinned unless a CVE forces the hand". Sequenced by risk, one upgrade = one commit = one gate, immediate rollback on red. Applied job6: ctx7 0.5.3→0.5.4, gsd-pi 2.64.0→3.0.0, gstack 070722a→11de390 (v1.52.1.0→v1.58.5.0), graphifyy binary 0.9.6→0.9.8 (hook-adoption declined separately, see below).
+- **Why**: job6-batch-3's expected verdict for gstack was KEEP-PINNED sauf CVE; user overrode it — a fail-open security-guard fix (#1911, no formal CVE) counts as the CVE clause in substance, and staying pinned to avoid work means carrying live-vulnerable tooling. Gating on integration tests (not on "did upstream file a CVE") catches the real risk (format/behavior breaks) that pin-forever also fails to prevent — gsd-pi 3.0.0 broke status-reporter's ROADMAP.md parser silently (0/0 instead of an error); the gate caught it before merge, KEEP-PINNED would have avoided the break but also frozen out #1688 (gsd-pi data-loss fix) and the gstack #1911 guards indefinitely.
+- **Alternatives rejected**: KEEP-PINNED unless CVE (job6-batch-3 default) — optimizes for zero-gate-work, pays for it by sitting on fail-open security guards and data-loss bugs with no formal CVE filed; blanket "always latest, no gate" — the gsd-pi break shows why the gate stays mandatory, this is not a license to skip it.
+- **Caveats**: not every dep took the full pull — graphifyy's hook-guard rewrite (a config-protected file) was surfaced with a diff and the user declined to adopt it this round (binary upgraded, hook install skipped); MCP magic version pin was declined by user call. Policy is "latest, gated", not "latest, no exceptions".
+- **Reference**: `.audit/job6-report.md`; commits `b4896c9` (gsd-pi), `2813e55` (gstack), `00c97bc` (docs); [[LRN-107]] (secrets-subagent value-copy ban, same job's incident).

.claude/memory/evals.md

@@ -189,3 +189,12 @@ rules:
 - **result**: `make test` grew from 71 (gitflow only, 5 suites excluded) to 90 gitflow + all 5 previously-excluded run-*.sh suites now included (13→16 deterministic, 32 doc-commit unchanged, 19→23 doc-shape, 20→25 reconcile, 5/5 release) + 4 *.test.sh grew or were added (20→24 config-protection, 0→6 curated-config-guard new, 13→16 deploy-commit, 0→1 toggle-external-repo-resolution new). Full `make test` exit 0 throughout, zero regression across 20 commits.
 - **anomalies**: (1) `/tmp` (tmpfs, 7.4G) exhausted mid-session from repeating full-repo `cp -r` (incl. `.git` + gstack submodule, ~1.6G each) for the first 4 specs' scratch copies — the Bash tool became universally unresponsive (even `true`/`echo` failed with exit 1/134) until the user cleared `/tmp` manually; switched to copying only the minimal file subset each mutation needs for the remaining ~16 specs/fixes. (2) config-protection.sh's guard matches by path SUFFIX regardless of directory, so scratch-copy mutations of `lib/gitflow.sh`/`hooks/*.sh` tripped it too even though they were throwaway and never committed — used Bash/sed/perl (shell-level file ops, which the hook's own header comment says it never covers) instead of Edit/Write for those mutations, reserving the sentinel strictly for genuine `lib/tests/` writes. (3) J4-22's caller census (an explicit gate in the report) found `deploy/SKILL.md` parses `deploy-commit.sh`'s exit codes — flagged before committing, user confirmed GO to extend that doc too rather than leaving it stale.
 - **action**: keep. Branch unmerged (`chore/job4-tests`, human gate per report). Backlog carried forward unbuilt, deliberately per report scope: J4-13 (rtk-rewrite), J4-14 full (session-start banner truth-table — only the offline-fetch seam landed), J4-15/16/17 (toggle-external 3-state/attribution-census/memory-commit pending verb), J4-18 (graphify pytest greenfield), and the hermetic suites the SEAMS bundle unlocked but didn't build for profile.sh/toggle-external.sh/design-tool-gate.sh (J4-19/20/21, now spec-able instead of UNTESTABLE).
+
+## EVAL-020 — job6 dep upgrade execution: 5 deps sequenced by risk, 2 real STOP gates hit and resolved live, zero regression
+
+- **Date**: 2026-07-07
+- **output**: `.audit/job6-report.md` execution — ctx7 0.5.3→0.5.4 (BATCH-1, zero repo diff), graphifyy binary 0.9.6→0.9.8 (hook-adoption declined), gsd-pi 2.64.0→3.0.0 (`b4896c9`), gstack submodule 070722a→11de390 (`2813e55`), supply-chain doc pass (`00c97bc`) — all on `chore/job6-deps-upgrade`, unmerged, human gate per report.
+- **method**: pre-flight gated on 2 user-confirmed prerequisites (gstack #2047 human review verdict, MAGIC_API_KEY rotation) before any step. Sequenced strictly by risk (BATCH-1 → BATCH-2 ascending); one upgrade = one commit = one gate (make test + named smoke), immediate STOP-and-ask on any ambiguous or destructive fork rather than assuming a default.
+- **result**: 2 real STOP conditions fired and were resolved live, not hypothetically: (1) graphifyy 0.9.8's `graphify install` traced to source (`_install_claude_hook`, pipx venv `__main__.py:2033`) confirmed as a REWRITE of the config-protected `.claude/settings.json` — diff shown, user declined, binary upgraded without hook adoption; (2) gsd-pi 3.0.0 confirmed format-INCOMPATIBLE with `status-reporter.md`'s ROADMAP.md parser by generating a real test milestone in a scratch dir (ADR-013 cutover: no ROADMAP.md at all, DB-authoritative) — user chose "patch now" over rollback, parser rewired to `gsd headless query` JSON, smoke-tested both the absent-`.gsd/` and real-`.gsd/` cases before commit. gstack's local playwright patch (BDR-029) correctly identified as disposable-by-design, backed up before discard anyway (belt-and-suspenders after an auto-mode classifier denial), reapplied via the documented `gstack_bump_playwright_if_unsupported` steps — landed one minor ahead (1.61.1 vs the pre-bump 1.61.0) since upstream had moved between backup and reapply. `make test` green after every commit (90/90 gitflow + suites); `doctor.sh` 0 errors throughout.
+- **anomalies**: (1) mid-session the Bash tool went universally unresponsive (`true`/`echo hello` returning non-zero, no output) right after a large heredoc `git commit` — same `/tmp` exhaustion class as [[EVAL-019]]'s anomaly (1), user confirmed and cleared it; work resumed from the last confirmed git state rather than blindly retrying. (2) MCP magic's requested "reference not plaintext" (BDR-026 pattern) turned out NOT achievable as literally asked — `${VAR}` env expansion is documented for project-scope `.mcp.json` only, not the global `~/.claude.json` where magic is registered `--scope user` (verified via 2 rounds of sourced doc lookup, not assumed); user accepted the practical ceiling (regenerate via `toggle-external.sh disable/enable` to refresh the rotated key, decline the version pin).
+- **action**: keep. Branch unmerged (`chore/job6-deps-upgrade`, gitflow finish = separate human signal per CLAUDE.md). [[BDR-056]] captures the policy reversal this run demonstrated; [[LRN-107]] captures the secrets-copy mandate gap the report's own incident surfaced.

.claude/memory/journal.md

@@ -349,3 +349,8 @@ rules:
 - job4 test-gap audit shipped read-only: `.audit/job4-report.md` — hooks/gitflow-guardrails/session-libs/reconcile-fixtures/graphify scope, 22 findings, 11 named specs + NOT-SAFE items, all fresh-context verified [[EVAL-019]]. run-*.sh 5 suites confirmed excluded from `make test` (J4-01, CRITICAL).
 - User GO full execution, decisions injected: J4-01 first commit (gate must lean on the fixed aggregator); J4-04+toggle-external fix authorized (red→fix→green, 2 commits each, diff shown before commit); deploy-commit new exit codes ≥6; sentinel pre-auth for lib/tests/ + steps 6-9 fixes; SPEC-06 held at explicit confirm despite AUTHORIZED line (ambiguity in user's own instructions, resolved by asking). Executor = this session on chore/job4-tests, NO finish.
 - job4 EXECUTED: 20 commits chore/job4-tests, all mutations red-green verified (scratch/lean copies, never the working tree), `make test` green throughout (71→90 gitflow + all 5 excluded suites now included). Incident: `/tmp` (tmpfs) exhausted from repeated full-repo `cp -r` (incl. `.git`+gstack submodule) → Bash universally broken until user cleared it; switched to minimal-file scratch copies for the rest. config-protection guards by path SUFFIX regardless of dir → scratch mutations of guarded-pattern files done via Bash/sed (shell ops, hook's own doc says it never covers those) not Edit/Write. J4-22 caller census found deploy/SKILL.md parses deploy-commit exit codes — flagged, user GO'd doc-sync too. [[LRN-106]] (B1-fix-≠-pattern-close, caught by job4 finding the exact same live-registry-read fragility job3 left in T3/T5 of the same file). Branch unmerged, human gate. Backlog: J4-13/14(partial)/15/16/17/18 + hermetic suites for profile/toggle-external/design-tool-gate (unlocked by SEAMS, not built).
+
+## 2026-07-07
+- job6 dep-upgrade audit shipped read-only: `.audit/job6-report.md` — rtk/gsd-pi/gstack/ctx7/graphifyy/semgrep/impeccable/emil/darwin/magic MCP census, BATCH-1/2/3 verdicts, 22 CONFIRMED/2 CORRECTED/0 REFUTED. Incident: explorer copied plaintext MAGIC_API_KEY into scratch, redacted post-check — [[LRN-107]].
+- User GO full execution, prerequisites confirmed upfront (gstack #2047 human review → pull complet + reapply local fix; MAGIC_API_KEY rotated). Sequenced by risk, one upgrade = one commit = one gate, chore/job6-deps-upgrade, no finish.
+- job6 EXECUTED: ctx7 0.5.3→0.5.4 (zero repo diff), graphifyy binary 0.9.6→0.9.8 (hook-guard rewrite of config-protected `.claude/settings.json` traced to source, diff shown, user declined adoption), gsd-pi 2.64.0→3.0.0 (`b4896c9` — 3.0.0 confirmed format-incompatible with status-reporter's ROADMAP.md parser via a real scratch-dir test milestone; ADR-013 cutover, DB-authoritative, no ROADMAP.md at all; user chose patch-now, parser rewired to `gsd headless query` JSON, smoke-tested both cases), gstack submodule 070722a→11de390 (`2813e55` — full pull per verdict, #1911 fail-open guards + PII/telemetry/data-loss fixes; local playwright patch (BDR-029) backed up then discarded then correctly reapplied via the documented bump function, landed one minor ahead since upstream moved meanwhile; /careful + /freeze smoke-tested blocking live), supply-chain docs (`00c97bc` — pipx-only graphifyy rule, semgrep p/* runtime-pack caveat; MCP magic version pin declined by user, `${VAR}` env-expansion confirmed unsupported at `~/.claude.json` user scope after 2 rounds of sourced doc lookup — BDR-026 pattern doesn't transfer there, regenerated live config instead via toggle-external.sh to pick up the rotated key). `make test` 90/90 green + `doctor.sh` 0 errors throughout. Incident: mid-session Bash tool universally unresponsive again post-`/tmp` exhaustion (same class as job4's), user cleared it, resumed from confirmed git state. [[EVAL-020]], [[BDR-056]] (deps policy reversal: latest gated by integration, not KEEP-PINNED default). Branch unmerged, human gate — orphan `~/skills-lock.json` (F-S1) also deleted, non-repo file, no commit.

.claude/memory/learnings.md

@@ -1084,3 +1084,11 @@ rules:
 - **context**: 2026-07-06, job3 chore/job3-fixes (B1 unblock) then job4 SPEC-10 (`.audit/job4-report.md` J4-10), same run-reconcile.sh, same session-day — closed for real this time (T3/T5 repointed at a new `decisions-snapshot.md` fixture, `$MEM` variable deleted, `grep -c '$MEM' == 0` gate).
 - **future application**: after fixing one instance of a "reads live state it shouldn't" (or any similarly generic) finding, grep the WHOLE FILE (and ideally the whole surface class) for the same pattern before declaring the class closed — not just the line/test the finding cited.
 - **cousin**: [[LRN-077]] (pin grep, don't trust one instance), [[BDR-041]] (reconcile design: verify don't believe).
+
+## LRN-107 — read-only subagent mandates must ban copying secret VALUES, not just mutations
+
+- **pattern**: job6 (2026-07-07), an explorer subagent under explicit no-execute/read-only mandate (LRN-105 class) copied the plaintext `MAGIC_API_KEY` value into its own scratch file while investigating the magic MCP config. Harness flagged it; main session redacted (1 occurrence, clean post-scan). The mandate said "don't mutate anything" — it never said "don't copy a secret's value into a NEW file you create", so a read-only agent still leaked a secret copy.
+- **why**: "read-only" naturally reads as "doesn't change existing state" — copying a value into a fresh scratch file isn't a mutation of anything that existed, so it doesn't trip that mental model, but it creates a brand new place the secret now lives (BDR-026's exact class: secrets have copies beyond the canonical store — tool configs, transcripts, caches, and now subagent scratch files too).
+- **context**: `.audit/job6-report.md` "Incident (contained)" section; explorer-C.md redacted post-incident; caught before job6's execution phase, contained to scratchpad only.
+- **future application**: any read-only/no-execute subagent mandate that touches config or env files must explicitly ban copying a secret's VALUE into agent output/scratch, not just ban editing/deleting. Phrase the mandate as "reference by name/location, never paste the value" — when auditing MCP/env config, prefer `jq 'del(.. | .env?)'`-style filtering (already BDR-026 practice) over raw `cat`.
+- **cousin**: [[BDR-026]] (secrets have copies, protect/audit them all), [[LRN-105]] (explorer no-execute mandate, the sibling rule this extends).

README.md

@@ -84,6 +84,11 @@ ctx7 login                 # optional: OAuth / API key for higher rate limits
 
 Versions are pinned in `plugins.lock.json`. To update: edit the file, then re-run `install-plugins.sh`.
 
+Graphify installs via **pipx/PyPI only, never npm/npx**: a different publisher
+squats the same `graphifyy` name on npm (version-shadowing shim re-exporting
+a different package, ships its own conflicting `graphify` bin) — see
+`plugins.lock.json`'s `graphifyy` note.
+
 ---
 
 ## Slash commands

agents/security-auditor.md

@@ -60,6 +60,10 @@ non-deterministic gate). owasp-top-ten is REQUIRED, not optional: measured
 2026-07-03, the two-ruleset baseline missed SQL injection and path traversal
 entirely on realistic Flask code; owasp-top-ten's taint rules catch them.
 
+Caveat: `p/*` packs are fetched from the registry at RUNTIME — pinning the
+`semgrep` CLI version (`plugins.lock.json`) does NOT freeze ruleset content;
+a new BLOCK can appear on unchanged code even with the CLI pin untouched.
+
 **Severity mapping** (from `results[].extra.severity` + ruleset origin):
 
 | semgrep | origin | → gate severity | blocks? |

agents/status-reporter.md

@@ -91,49 +91,38 @@ If no test infrastructure found:
 
 ---
 
-## PHASE 3 — GSD v2 STATUS (if .gsd/ exists)
+## PHASE 3 — GSD STATUS (if .gsd/ exists)
+
+gsd-pi ≥3.0.0 (ADR-013 cutover): the DB is authoritative, `.gsd/ROADMAP.md`
+no longer exists (state moved to `.gsd/STATE.md`, `.gsd/gsd.db`, and one
+`.gsd/milestones/<ID>/<ID>-ROADMAP.md` per milestone). Read state through the
+CLI's own structured snapshot instead of scraping markdown.
 
 ```bash
-# Check .gsd/ presence and contents
+# Check .gsd/ presence
 ls .gsd/ 2>/dev/null | head -10
 
-# ROADMAP.md — milestone checklist (most reliable source)
-cat .gsd/ROADMAP.md 2>/dev/null | head -60 || echo "no ROADMAP.md"
-
-# Slice-level progress — GSD v2 uses ### headings for slices (not tasks)
-# Slices done = ### headings with [x] marker
-grep -c '^### .*\[x\]' .gsd/ROADMAP.md 2>/dev/null || echo "0"
-# Slices total = all ### headings
-grep -c '^### ' .gsd/ROADMAP.md 2>/dev/null || echo "0"
-
-# Task-level count (informational only — not the primary progress metric)
-# Done tasks: - [x], Total tasks: - [
-grep -c '^\s*- \[x\]' .gsd/ROADMAP.md 2>/dev/null || echo "0"
-grep -c '^\s*- \[' .gsd/ROADMAP.md 2>/dev/null || echo "0"
-
-# Current milestone — tries slice-level first, falls back to task-level
-# Primary: first ## heading with a ### slice without [x]
-awk '/^## /{ms=$0} /^### /{if(index($0,"[x]")==0){print ms; exit}}' .gsd/ROADMAP.md 2>/dev/null
-# Fallback (flat structure — tasks directly under ##, no ### slices):
-# Scoped to ## Milestone headings only — avoids matching documentation lists
-# Resets on any non-Milestone ## heading (e.g. ## Prerequisites, ## Notes)
-awk '/^## [Mm]ilestone/{ms=$0} /^## / && !/[Mm]ilestone/{ms=""} /^- \[/{if(ms && index($0,"- [x]")==0){print ms" (flat)"; exit}}' .gsd/ROADMAP.md 2>/dev/null
-# All ## headings for context
-grep -E '^## ' .gsd/ROADMAP.md 2>/dev/null
-
-# Any additional GSD state files
-find .gsd/ -name "*.md" -not -name "ROADMAP.md" 2>/dev/null | head -5
+# Structured snapshot — no LLM call, no markdown scraping
+gsd headless query 2>/dev/null || echo "no gsd query output"
 ```
 
 **Reading the output:**
-- If `ROADMAP.md` exists: derive progress at **slice level** (### headings), not task level.
-  Slices done = `### headings with [x]`. Slices total = all `### headings`.
-  Report as: "X/Y slices done" — this matches GSD v2's own progress dashboard.
-  The current milestone = first `## heading` with an unchecked `### slice`. If no `###` slices exist (flat structure with tasks directly under `##`), fall back to the first `## heading` with an unchecked `- [ ]` task (second awk command, marked with "(flat)"). If both return empty, all milestones are complete.
-- If only `.gsd/` exists but no `ROADMAP.md`: GSD initialized but no roadmap yet.
-  Print: "GSD v2 initialized — no ROADMAP.md yet. Run `/gsd init` or `/gsd discuss` to create one."
-- If `.gsd/` is absent: print "GSD v2 not initialized for this project."
-- Never attempt to read `state.db` or binary files — print "N/A" if state unclear.
+- If `.gsd/` is absent: print "GSD not initialized for this project."
+- If `.gsd/` exists but the query errors or prints nothing: GSD initialized but
+  unreadable — print "GSD initialized — query failed, run `gsd headless status`
+  for a human-readable dashboard."
+- Otherwise parse the JSON:
+  - `progress.slices.done` / `progress.slices.total` → report as "X/Y slices
+    done" (matches GSD's own dashboard; this is the primary progress metric).
+  - `progress.milestones.done` / `progress.milestones.total` for milestone-level.
+  - `state.activeMilestone.title` / `state.activeSlice.title` → current
+    milestone/slice. Both `null` means nothing active (not started, or all
+    milestones complete — disambiguate via `progress.milestones`).
+  - `state.nextAction` → print verbatim as the next step.
+  - `state.blockers` → if non-empty, surface each one.
+- Never read `.gsd/gsd.db` directly (SQLite, not markdown) or treat
+  `.gsd/` as a local directory for backup/copy purposes — it may be a symlink
+  to `~/.gsd/projects/<hash>/` (out-of-tree state store).
 
 ---
 

plugins.lock.json

@@ -7,13 +7,13 @@
   },
   "gsd": {
     "source": "npm:gsd-pi",
-    "version": "2.64.0",
-    "note": "Check latest at https://www.npmjs.com/package/gsd-pi before updating. GSD v2 is a standalone CLI (Pi SDK), not a Claude Code plugin. Run 'gsd' in terminal, not '/gsd' in Claude Code. NOTE: update-all.sh honors this pin — 'make update' will NOT advance gsd past it; bump this version deliberately, then re-run."
+    "version": "3.0.0",
+    "note": "Check latest at https://www.npmjs.com/package/gsd-pi before updating. GSD is a standalone CLI (Pi SDK), not a Claude Code plugin. Run 'gsd' in terminal, not '/gsd' in Claude Code. ADR-013 cutover (3.0.0): DB is authoritative, .gsd/ROADMAP.md no longer exists — read state via 'gsd headless query' (see agents/status-reporter.md PHASE 3), not markdown scraping. NOTE: update-all.sh honors this pin — 'make update' will NOT advance gsd past it; bump this version deliberately, then re-run."
   },
   "gstack": {
     "source": "https://github.com/garrytan/gstack.git",
     "managed_by": "git submodule",
-    "note": "Version controlled by submodule pointer in .gitmodules. Update: git submodule update --remote"
+    "note": "Version controlled by submodule pointer in .gitmodules. Update: git submodule update --remote. Pinned at 11de390 (v1.58.5.0, job6): pulled deliberately for the #1911 fail-open security-guard fix (careful/guard/freeze/data-loss guards) after human review of #2047 (gbrowser stealth, accepted). Local playwright bump (BDR-029, BLK-008) is reset by every submodule update and re-applied by install-plugins.sh's gstack_bump_playwright_if_unsupported()."
   },
   "ctx7": {
     "source": "npm:ctx7",
@@ -24,7 +24,7 @@
     "source": "pypi:graphifyy",
     "version": "latest",
     "managed_by": "pipx",
-    "note": "Codebase knowledge graph. CLI is 'graphify'. Install: pipx install graphifyy && graphify install && graphify claude install. Adds PreToolUse hook for Glob/Grep."
+    "note": "Codebase knowledge graph. CLI is 'graphify'. Install: pipx install graphifyy && graphify install && graphify claude install. Adds PreToolUse hook for Glob/Grep. pipx/PyPI ONLY — never npm/npx: a different publisher (rhanka/graphify) squats the same 'graphifyy' name on npm, a version-shadowing shim with its own conflicting 'graphify' bin."
   },
   "semgrep": {
     "source": "pypi:semgrep",