feat(kits)!: adopt pinned agent and capability kits

.github/workflows/pre-commit.yml

@@ -64,5 +64,7 @@ jobs:
             pre-commit-${{ runner.os }}-
       - name: Install pre-commit
         run: python -m pip install pre-commit
+      - name: Install markdown linter dependencies
+        run: npm ci --prefix .github/linters
       - name: Run pre-commit
         run: pre-commit run --all-files --show-diff-on-failure --color=always

.pre-commit-config.yaml

@@ -110,7 +110,7 @@ repos:
         entry: bash scripts/test-acq-bats
         language: system
         pass_filenames: false
-        files: '^(acq|acq\.backends/.*|scripts/test-acq-lib\.sh|scripts/test-acq-bats|test/bats/.*)$'
+        files: '^(acq|acq\.backends/.*|scripts/test-acq-lib\.sh|scripts/test-acq-bats|scripts/fix-exec-bits|scripts/verify-backends|test/bats/.*)$'
 
       # Lint the .bats files with ShellCheck (it treats .bats as a shell dialect).
       # The main shellcheck hook's `types: [shell]` does not reliably tag .bats,
@@ -121,3 +121,26 @@ repos:
         entry: bash -c 'printf "%s\n" "$@" | xargs -r -n8 shellcheck --severity=warning' --
         language: system
         files: '^test/bats/.*\.(bats|bash)$'
+
+  # Guard the executable bit the git index records for entry points.
+  #
+  # The repo is routinely checked out onto a container/host shared mount
+  # (virtiofs, Docker Desktop sharing, WSL drvfs) where the host clone sets
+  # core.fileMode=false to suppress spurious mode churn. That makes git BLIND to
+  # a LOST exec bit: a 100755 -> 0644 regression with identical content produces
+  # an empty `git status` and an empty `git diff --summary`. Since nearly every
+  # editor/formatter/agent writes a temp file and renames it (new inode, ambient
+  # umask), entry points silently stop being executable and the next live run
+  # fails with rc=126 — or, worse, with a misleading downstream error.
+  #
+  # --check reports and fails; `scripts/fix-exec-bits` repairs. It compares
+  # against the INDEX, so sourced libraries (acq.backends/*.sh) and bats files
+  # stay correctly non-executable; a shebang is not the criterion.
+  - repo: local
+    hooks:
+      - id: fix-exec-bits
+        name: executable bits match the git index
+        entry: bash scripts/fix-exec-bits --check
+        language: system
+        pass_filenames: false
+        always_run: true

CONTRIBUTING.md

@@ -107,6 +107,7 @@ npm ci --prefix .github/linters
 | `npm run lint` | Run all linters |
 | `npm run lint:secrets` | Run gitleaks at the version pinned in `.pre-commit-config.yaml` (pre-commit fetches it; no separate install) |
 | `npm run check` | Run the full pre-commit suite (gitleaks, shellcheck, YAML/JSON validation, whitespace, markdown lint) |
+| `npm run fix:exec-bits` | Restore executable bits the git index records (see below) |
 
 > [!NOTE]
 > `npm run check` auto-fixes some issues (markdown, whitespace, EOF) — review and stage the changes it makes.
@@ -118,6 +119,40 @@ kits it applies — and their tests (permission-matrix, model-sync, per-kit
 repo under `integrations/isolation/acq-kits/`. Changes to provider config,
 rules, skills, or CA trust belong there.
 
+### If a script suddenly says "Permission denied"
+
+Run:
+
+```bash
+npm run fix:exec-bits      # or: scripts/fix-exec-bits
+```
+
+Clones on a **container/host shared mount** (virtiofs, Docker Desktop file
+sharing, WSL drvfs) do not round-trip POSIX permissions reliably, so such clones
+typically set `core.fileMode = false` to stop git reporting a storm of spurious
+mode changes. That is the right call, and it creates a blind spot:
+
+- git applies the index mode on **checkout**, so a fresh clone is correct;
+- but almost every editor, formatter, and coding agent saves by writing a temp
+  file and renaming it. That is a **new inode** with the ambient umask (0644),
+  so the executable bit is gone;
+- with `core.fileMode = false`, git is **blind** to that. A 100755 → 0644
+  regression with identical content yields an empty `git status` *and* an empty
+  `git diff --summary`.
+
+The symptom is an entry point that stops working with no visible cause —
+`./scripts/verify-backends` exiting 126, or the vendored bats failing several
+execs deep (`bin/bats` re-execs `libexec/bats-core/bats`, which execs
+`bats-exec-suite` and a formatter, so a stripped bit surfaces as a confusing
+downstream error rather than an obvious permission one).
+
+`scripts/fix-exec-bits` compares every tracked file against its **index** mode
+and restores the bit. The index is the criterion, not the presence of a shebang:
+`acq.backends/*.sh` are *sourced* and `test/bats/*.bats` are read *by bats*, so
+both are correctly non-executable. It covers initialized submodules too, and
+`--check` makes it report-only (that form runs as a pre-commit hook, and
+`scripts/verify-backends` self-heals at startup).
+
 There is one offline unit suite (stubbed `sbx`/`msb`/`opencode`, no Docker or
 network), built on [bats-core](https://github.com/bats-core/bats-core) (ADR-0025):