fix(kyberforge): bridge apm content to Claude Code's flat plugin discovery

Claude Code's (and Copilot's) native plugin installer has zero awareness of
.apm/ nesting -- it convention-scans only flat skills/, agents/, commands/,
hooks.json at each plugin's root. Confirmed via strings on the installed
claude binary and live installs of git@holocron/gitea@holocron/kyberforge@
holocron, all reporting Skills(0) Agents(0) Hooks(0) post ADR-0015's apm
conversion. Root cause (apm_cli/core/plugin_manifest.py): apm's plugin.json
compiler deliberately strips skills/agents/commands keys, assuming the host
already auto-discovers those convention directories -- it has no model of
.apm/ being host-visible at all. Separately, apm's own bundle exporter
(apm_cli/bundle/plugin_exporter.py, behind `apm pack --format plugin`)
implements the correct .apm/ -> flat mapping, but only ever targeted
build/<name>-<version>/, a path nothing in marketplace.json's source: points
at.

scripts/sync-plugin-content.sh wraps that bundle exporter and copies its
agents/, skills/, commands/, instructions/, extensions/, and merged
hooks.json back into each plugin's own root as a second tracked
compiled-output category -- same governance status as
.claude-plugin/plugin.json: generated from .apm/, never hand-edited. tests/
subdirectories are excluded from the mirror (dev fixtures, not host-visible
runtime content; several hardcode a relative repo-root walk-up sized for the
.apm/-nested depth, which breaks when duplicated one level shallower).
Applied for real across all 6 plugins and verified two ways: `claude plugin
validate --strict` passes on every real plugin directory, and a live
`claude --plugin-dir <path> -p "list skills/agents"` behavioral test
confirms content is now actually discovered.

Also, from the same issue #90 review round:
- scripts/check-manifests.sh pointed at each plugin's root-level plugin.json
  (checking skills/hooks/mcpServers/agents pointer fields) -- that file was a
  stale near-duplicate of .claude-plugin/plugin.json nothing else read or
  wrote, now deleted across all 6 plugins. check-manifests.sh is rewritten to
  validate .claude-plugin/plugin.json instead, and drops the pointer-field
  checks entirely (nothing to check -- those fields are correctly absent by
  design). Content-presence drift is now check-plugin-content-sync's job, a
  new pre-push hook wired in .pre-commit-config.yaml.

docs/adr/0017 records the root cause and decision in full, including two
rejected alternatives (patching plugin.json's path fields directly -- apm's
compiler strips them on every run; pointing marketplace.json at apm pack's
build/ output -- a version-suffixed non-source directory nothing can install
from without an extra build step). ADR-0015 and CONTEXT.md are updated to
point at it.

Refs: #90

plugins/git/skills/pc-run/README.md

@@ -0,0 +1,29 @@
+# pc-run
+
+Runs, installs, updates, and maintains pre-commit hooks in a local git clone.
+
+## What it does
+
+`pc-run` handles everything that happens *after* `.pre-commit-config.yaml` exists: wiring hooks into git, running them, bumping their versions, and maintaining the cache. When hooks fail, it identifies the cause and suggests a concrete fix — it does not auto-fix files or edit the config. For creating or editing `.pre-commit-config.yaml`, use `pc-author` instead.
+
+## Before you start
+
+- `pre-commit` must be installed and available on `PATH`
+- A `.pre-commit-config.yaml` must exist at the repo root (use `pc-author` to create one)
+
+## Usage
+
+Common invocations:
+- `/pc-run` — run all hooks against all files (default)
+- `/pc-run install` — wire hooks into `.git/hooks/`
+- `/pc-run autoupdate` — bump all `rev` values to latest
+- `/pc-run clean` — wipe the pre-commit cache (requires confirmation)
+
+## Files
+
+| File | Purpose |
+|------|---------|
+| `SKILL.md` | Skill instructions for agents |
+| `references/failure-patterns.md` | Hook failure causes and concrete fix suggestions |
+| `references/sources.md` | Provenance: research sources that informed this skill |
+| `references/README.md` | Directory index for references/ |

plugins/git/skills/pc-run/SKILL.md

@@ -0,0 +1,123 @@
+---
+name: pc-run
+description: >
+  Use when the user wants to run pre-commit hooks, install git hooks, update
+  hook versions, or maintain the pre-commit cache. Triggers on: "run
+  pre-commit", "run all hooks", "check everything passes", "install hooks",
+  "wire hooks into git", "update hook versions", "autoupdate", "bump revs",
+  "clean the cache", "rebuild environments", "gc", "why is my hook failing",
+  "hooks aren't running". Do not use for creating or editing
+  `.pre-commit-config.yaml` — use `pc-author` for that.
+
+compatibility: Requires pre-commit installed and available on PATH.
+
+metadata:
+  category: devtools
+  source_keys:
+    - context7-pre-commit-com
+    - pre-commit-com
+
+allowed-tools: Bash Read
+---
+
+## Gotchas
+
+- Hooks not running on `git commit` almost always means `pre-commit install` was never run in this clone. Git hooks are per-clone — they are not committed to the repo.
+- When a hook modifies files (e.g. `trailing-whitespace`, `end-of-file-fixer`), the commit is blocked intentionally — the staged version is stale. The fix is `git add -u && git commit`. Do NOT call `pre-commit install -f` here; that is for overwriting existing hooks, not re-staging.
+- `pre-commit autoupdate` modifies `.pre-commit-config.yaml` in-place. Re-read the file after calling it to show the user the updated `rev` values.
+- The `SKIP` env var requires exact hook `id` values, comma-separated, no spaces: `SKIP=check-yaml,gitleaks git commit -m "msg"`. A space after the comma silently skips nothing.
+- Never use `git commit --no-verify` (or `-n`) to bypass a failing hook. Hooks are the automated QA gate; bypassing them breaks the pipeline. Diagnose and fix the failure instead — see the hook-specific guidance below and in `references/failure-patterns.md`.
+- A stages mismatch — hook stage not installed — means the hook was added to the config but `pre-commit install` was not re-run with the correct `-t` flags. Hooks in stages not listed under `default_install_hook_types` will never fire.
+
+## Route
+
+Determine intent from the user's request, then execute the matching operation:
+
+| User intent | Operation |
+|---|---|
+| "run", "check", "verify", "test hooks" | `pre-commit run --all-files` (default) |
+| "staged", "simulate commit" | `pre-commit run` (staged files only) |
+| "CI", "changed files only", "diff range" | `pre-commit run --from-ref <base> --to-ref <head>` — prefer this over `--all-files` on large repos |
+| "install", "set up hooks", "wire into git" | `pre-commit install` — see Install |
+| "pre-create environments", "install-hooks", "warm cache" | `pre-commit install-hooks` — see Install |
+| "remove hooks", "uninstall", "tear down pre-commit" | `pre-commit uninstall` |
+| "autoupdate", "update versions", "bump revs" | `pre-commit autoupdate` |
+| "gc", "garbage collect" | `pre-commit gc` |
+| "clean", "wipe cache", "rebuild from scratch" | `pre-commit clean` — see Clean |
+
+If the intent is ambiguous, default to `pre-commit run --all-files`.
+
+## Run
+
+Default: `pre-commit run --all-files`. Never silently run staged-only.
+
+```bash
+pre-commit run --all-files
+```
+
+**When hooks fail**, read the output and:
+1. Identify which hook failed and the specific cause. Be concrete: "gitleaks blocked `config.json` (high-entropy string on line 12)", not just "gitleaks failed".
+2. Suggest a concrete next step. Common patterns are in `references/failure-patterns.md`.
+3. Do NOT auto-fix code files. Do NOT modify `.pre-commit-config.yaml`. Those are the user's or `pc-author`'s responsibility.
+
+If the user asks to run only staged files: `pre-commit run` (no `--all-files`).
+If the user names a specific hook: `pre-commit run <hook-id>`.
+
+## Install
+
+Only run when the user explicitly asks to install or set up hooks.
+
+Before running, check for existing hook files:
+
+```bash
+ls .git/hooks/
+```
+
+If any hook files exist (e.g. a hand-written `pre-commit`), `pre-commit install` does NOT refuse or error — it defaults to migration mode, which runs the existing hook and pre-commit's hooks both. Only `-f` replaces the existing hook file outright, and that replacement is not reversible via `pre-commit uninstall` — uninstall only removes pre-commit from `.git/hooks/`, it does not restore whatever hand-written hook `-f` overwrote. If files are present, tell the user: "Existing hook files found at `.git/hooks/<names>`. Plain `pre-commit install` will run both; `pre-commit install -f` will overwrite them permanently instead. Proceed with plain install, or overwrite?" Wait for confirmation before using `-f`.
+
+```bash
+pre-commit install
+```
+
+Re-run with `-t` flags when `default_install_hook_types` was changed or when hooks in non-default stages aren't firing:
+
+```bash
+pre-commit install -t pre-commit -t pre-push -t commit-msg
+```
+
+To pre-create all hook environments without running hooks (useful for CI warm-up or first-time setup):
+
+```bash
+pre-commit install-hooks
+```
+
+To remove pre-commit from `.git/hooks/` entirely:
+
+```bash
+pre-commit uninstall
+```
+
+## Autoupdate
+
+```bash
+pre-commit autoupdate
+```
+
+After it completes, read `.pre-commit-config.yaml` and report which `rev` values changed. If the user wants to pin to exact SHAs (for reproducibility): `pre-commit autoupdate --freeze`.
+
+## Clean and GC
+
+**`gc`** — removes only unused cached environments. Safe to run at any time:
+```bash
+pre-commit gc
+```
+
+**`clean`** — wipes the entire cache at `~/.cache/pre-commit`. All hook environments will be re-downloaded on next run. Require explicit confirmation before running:
+
+> "This will wipe the entire pre-commit cache. All hook environments will be re-downloaded on next run. Proceed?"
+
+Wait for the user to say yes before executing:
+
+```bash
+pre-commit clean
+```

plugins/git/skills/pc-run/references/README.md

@@ -0,0 +1,14 @@
+---
+source_keys:
+  - context7-pre-commit-com
+  - pre-commit-com
+  - context7-pre-commit-hooks
+  - pre-commit-hooks-github
+---
+
+# references/
+
+| File | Purpose |
+|---|---|
+| `failure-patterns.md` | Hook failure causes and concrete fix suggestions — loaded when hooks fail |
+| `sources.md` | Provenance: research sources that informed this skill |

plugins/git/skills/pc-run/references/failure-patterns.md

@@ -0,0 +1,130 @@
+---
+source_keys:
+  - context7-pre-commit-com
+  - pre-commit-com
+---
+
+# Hook Failure Patterns
+
+Common hook failure causes and concrete next-step suggestions.
+
+## Hook modified files — commit blocked
+
+Cause: A fixer hook (e.g. `trailing-whitespace`, `end-of-file-fixer`, `pretty-format-json`) modified staged files. The commit is blocked because the staged version is now stale.
+
+Fix: Re-stage and recommit.
+```bash
+git add -u
+git commit -m "same message"
+```
+
+## Secret detected (gitleaks)
+
+> Not sourced from the pre-commit research corpus (`context7-pre-commit-com`/`pre-commit-com` cover pre-commit itself, not gitleaks) — general tool knowledge, verify against gitleaks' own docs if precision matters.
+
+Cause: gitleaks found a high-entropy string or known secret pattern in a staged file.
+
+Suggestions:
+- If it's a false positive: add a `# gitleaks:allow` inline comment, or add the path to `.gitleaksignore`.
+- If it's a real secret: remove it from the file, rotate the credential, then commit.
+
+## Shellcheck warning
+
+> Not sourced from the pre-commit research corpus — general tool knowledge, verify against shellcheck's own docs if precision matters.
+
+Cause: shellcheck found a shell script issue. The output includes the file path, line number, and SC-code.
+
+Fix: Look up the SC-code on shellcheck.net or pass `--explain SCxxxx` to shellcheck for a detailed explanation. The most common fixes:
+- SC2086 (unquoted variable): wrap in double quotes.
+- SC2046 (unquoted command substitution): wrap in double quotes.
+- SC2181 (check exit code of `$?`): use `if command; then` directly.
+
+## `check-hooks-apply` fails
+
+Cause: A hook's `files`/`types` filter matches zero files in the repo — the hook is dead weight.
+
+Fix: Broaden the filter, or remove the hook if it no longer applies to this repo.
+
+## `check-useless-excludes` fails
+
+Cause: An `exclude` pattern matches no files.
+
+Fix: Remove or fix the pattern.
+
+## SSH cloning fails in CI
+
+Cause: The CI environment lacks SSH credentials to clone hook repos over SSH.
+
+Fix: Export `SSH_AUTH_SOCK` in the CI environment, or switch hook repo URLs to HTTPS.
+
+## HTTP proxy needed
+
+Cause: The CI/sandbox network requires a proxy to reach hook repos.
+
+Fix:
+```bash
+export http_proxy=http://proxy.example.com:3128
+export https_proxy=http://proxy.example.com:3128
+export no_proxy=localhost,127.0.0.1
+```
+
+## `rev` is a branch name — `autoupdate` broke it
+
+Cause: Branch refs are mutable and drift over time; pre-commit resolves them once at install time, so pinning to a branch name (instead of a tag or commit SHA) leads to silent version drift.
+
+Fix:
+```bash
+pre-commit autoupdate     # finds the latest tag and rewrites rev in place
+```
+
+## pretty-format-json fails but doesn't fix
+
+Cause: `pretty-format-json` requires `args: [--autofix]` to modify files. Without it, the hook only fails.
+
+Fix: The user (or `pc-author`) must add `args: [--autofix]` to the hook override in `.pre-commit-config.yaml`.
+
+## Environment stale or broken
+
+Cause: A hook's cached environment is corrupted or out of date.
+
+Fix:
+```bash
+pre-commit clean          # wipe all environments
+pre-commit install-hooks  # rebuild everything
+```
+
+Or less destructively:
+```bash
+pre-commit gc             # remove only unused environments
+```
+
+## Hooks don't run on `git commit`
+
+Cause: `pre-commit install` was never run in this clone.
+
+Fix: `pre-commit install`. Git hooks are per-clone — they are not committed to the repo.
+
+## Hook runs but matches wrong files (or no files)
+
+Cause: The `files:` pattern uses `re.search()` not full-string match. A pattern that looks correct may match unexpectedly.
+
+Diagnosis: `identify-cli <filename>` shows the type tags for a file. Verify `types:` filters against these.
+
+## stages mismatch — hook never fires
+
+Cause: Hook is defined for a stage (e.g. `pre-push`) but `pre-commit install` was not run with `-t pre-push`.
+
+Fix:
+```bash
+pre-commit install -t pre-commit -t pre-push -t commit-msg
+```
+
+Or add `default_install_hook_types` to `.pre-commit-config.yaml` and re-run `pre-commit install`.
+
+## `validate-config` schema error
+
+Common causes:
+- Missing `id` under a hook block
+- Missing `rev` under a non-local repo block
+- `repo: local` hook missing `language` or `entry`
+- Indentation error (valid YAML but invalid pre-commit schema)

plugins/git/skills/pc-run/references/sources.md

@@ -0,0 +1,33 @@
+# Sources
+
+## context7-pre-commit-com
+
+- **URL:** context7:/pre-commit/pre-commit.com
+- **Description:** Official pre-commit.com documentation — installation, configuration schema, CLI reference, hook authoring, advanced features, troubleshooting
+- **Contributing files:** SKILL.md, references/failure-patterns.md
+- **Research doc:** plugins/git/docs/research/docs/pre-commit/{overview,cli-reference,troubleshooting}.md
+- **Status:** `extracted`
+
+## pre-commit-com
+
+- **URL:** https://pre-commit.com/
+- **Description:** Pre-commit framework homepage — full docs covering install, config, CLI, hook authoring, stages, local hooks, meta hooks, hazmat helpers, CI integration
+- **Contributing files:** SKILL.md, references/failure-patterns.md
+- **Research doc:** plugins/git/docs/research/docs/pre-commit/{overview,cli-reference,troubleshooting}.md
+- **Status:** `extracted`
+
+## context7-pre-commit-hooks
+
+- **URL:** context7:/pre-commit/pre-commit-hooks
+- **Description:** Official pre-commit-hooks collection — all available hook IDs with options and examples
+- **Contributing files:** (none)
+- **Research doc:** plugins/git/docs/research/docs/pre-commit/hooks-reference.md § "pre-commit-hooks (official collection)"
+- **Status:** `extracted`
+
+## pre-commit-hooks-github
+
+- **URL:** https://raw.githubusercontent.com/pre-commit/pre-commit-hooks/main/README.md
+- **Description:** Official pre-commit-hooks README — complete hook listing with all args, categories, deprecated hooks, and latest version
+- **Contributing files:** (none)
+- **Research doc:** plugins/git/docs/research/docs/pre-commit/hooks-reference.md § "pre-commit-hooks (official collection)"
+- **Status:** `extracted`