Upstream skill refresh, present in the working tree before this session —
committed here rather than left dangling. Not authored work.
- uv invocation fix: `uv tool run graphifyy python` -> `uv tool run --from
graphifyy python`. Without --from, uv resolved the command name against
the package instead of running the interpreter.
- default output is now HTML viz; --obsidian opts into the vault.
- description reworded to trigger on codebase questions generally, not
only when graphify-out/ already exists.
Startup emitted 15 warnings: "Write(**/.env) is not matched by file
permission checks — only Edit(path) rules are."
Write(path) rules never matched. The 5 secret-file write bans were dead
config — .env, secrets/**, *.pem, *.key were freely writable. Converting
to Edit() makes them enforced: permissions.md:242 "Edit rules apply to all
built-in tools that edit files", and :244 prescribes exactly this ("add an
Edit deny rule for paths no tool may change").
- settings.json: Write(...) -> Edit(...) on the 5 patterns.
- Mirror the 9 secret patterns Read denied but Edit did not: *.p12, *.pfx,
id_rsa*, id_ed25519*, .ssh/**, credentials, credentials.json,
.aws/credentials, .azure/**. Read/Edit parity now 14/14. Claude could
previously overwrite an SSH private key or ~/.aws/credentials.
- New read-allowed/write-denied class: lockfiles (*.lock,
package-lock.json, pnpm-lock.yaml, go.sum) + node_modules/**. Reading
aids diagnosis; hand-editing is always wrong — the package manager
regenerates them via Bash, which Edit deny does not block.
- templates/settings/SETTINGS.md taught the broken Write() pattern; fixed
at the source so /onboard stops propagating it.
Rule syntax has no negation and deny beats allow, so deny globs cannot
carry exceptions — see the .env.example conflict noted in the follow-up.
STEP 1-8 preserved byte-for-byte; STEP 9-16 replaced by a doc-gen orchestration
that resolves all interaction (questions, NAP, precheck, overwrite, client-name),
assembles the PACKAGE, and dispatches handover-doc-writer. Dropped the inert
model: opus pin (inherits the big session model via inline-load).
code-cleaner is now a pure fix executor (was audit+gate+execute). Reroute the two
read-only-audit consumers (onboard STEP 6, tour Phase B) to a big-model agent
(general-purpose/analyzer) — an audit must stay on the big model, never the sonnet
executor. Refactor now runs on sonnet inside the executor (inline-load pin was inert).
Reroute hotfix's deeper-bug escalation to the /bugfix skill (bugfixer is now a
pure executor, not loadable standalone). loops-light locks repointed to the
bugfix orchestrator + bugfixer-executor shape.
Bastien Chanot