fix(factory-audit): flag unbraced plugin-root tokens and close hook check gaps

Why: PR #144 review round 4 reproduced hooks referencing $PLUGIN_ROOT or
${PLUGIN_ROOT} without a path separator passing the audit, although apm
only rewrites ${TOKEN}/ and the deployed hook points nowhere.

- FAIL unbraced or unseparated plugin-root tokens
- check the exec bit for scripts run via an interpreter -c string
- skip env NAME=value prefixes when locating bare relative paths
- correct input: and empty-frontmatter messages, depth-walk applyTo braces
- INFO on unrecognised targets; failing-case tests for untested checks
- document tiers, blind spots and crash exit 2; drop rtk from portable flow
- restore the after-a-hand-edit trigger; pin upstream apm source URL

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01KkT7RSDwDbmrM9T34b6sTi

plugins/kyberforge/.apm/skills/factory-audit/references/hook-flow.md

@@ -25,17 +25,41 @@ Resolve the path against this skill's own directory. Run exactly:
 bash scripts/validate.sh <hook-file>
 ```
 
-Its findings become the `### Structure` dimension, FAILs and SUGGESTIONs both, at the tier the script assigned: JSON validity, the wrapped-or-naked shape, event lists and nested handler lists (the checks whose failure makes the Copilot install fail), a file contributing no entries (no events, only empty event lists, or an entry with no handler), event names that never fire, unfilled `FILL IN` or `FILL_IN_` template placeholders, a symlinked file or one under apm's deployed output rather than package source, referenced scripts that are missing, outside the package, not executable when run directly, or referenced by an absolute, bare relative, `../`, split-quoted, space-containing, or `$`/backtick-containing path apm will not bundle correctly, deprecated filename routing, and `${CLAUDE_PLUGIN_ROOT}` where `${PLUGIN_ROOT}` would do. Script references are read with apm 0.28.0's own patterns: `${PLUGIN_ROOT}/…` only when the path follows the token directly, up to the first whitespace or quote, and `./…` anywhere in the command. A `./` or `../` match is held to the script rules — a FAIL when missing — only in command position (the first token, or the first operand after `bash`, `sh`, `zsh`, `python`, `python3`, `node`, `pwsh`, `ruby` or `perl`, past its options such as `-e` or `-u`; after a `sh`-family `-c`, the first token of the command string; inline code such as `python3 -c` has none), when it ends in a script extension, or when it names a package entry that is not a file; any other match (`npx prettier --check ./src`, `printf '.\n'`) is at most a SUGGESTION, because apm only warns and it runs against the consumer's working directory as meant. Absolute and bare relative script paths are checked in the same command positions. Each event is judged per target the package root's `apm.yml` deploys to — no `target:`/`targets:`, `all`, or no `apm.yml` means every hook target — after apm's rename map for that target: it FAILs when a target with a published event list (Claude, Copilot) does not fire the renamed name, whatever its casing. It exits **0** with no FAIL, **1** on real findings, **2** when it never ran — report that as `### Structure` unverified, quoting the stderr reason. An INFO line is observational: report it under `### Structure` and count it in `· P info`.
+Its findings become the `### Structure` dimension, FAILs and SUGGESTIONs both, at the tier the script assigned.
+
+Checks:
+
+- JSON validity and UTF-8 encoding; a top level that is not a JSON object; the wrapped-or-naked shape; event lists and nested handler lists (the checks whose failure makes the Copilot install fail).
+- A file contributing no entries (no events, only empty event lists, or an entry with no handler), an empty event name, and event names that never fire.
+- Unfilled `FILL IN` or `FILL_IN_` template placeholders.
+- A symlinked file, or one under apm's deployed output or outside any package rather than package source (exit 1, a finding, not exit 2).
+- Referenced scripts that are missing, outside the package, not executable when run directly, or referenced by an absolute, bare relative, `../`, split-quoted, space-containing, or `$`/backtick-containing path apm will not bundle correctly.
+- A plugin-root token apm never rewrites: unbraced (`$PLUGIN_ROOT/x.sh`, `$CLAUDE_PLUGIN_ROOT`), or braced but not directly followed by `/` or `\` (`cd ${PLUGIN_ROOT} && …`).
+- Deprecated filename routing, and `${CLAUDE_PLUGIN_ROOT}` where `${PLUGIN_ROOT}` would do.
+- INFO: no `apm.yml` at an inferred `.apm/` package root, or a `targets:` naming no hook target apm recognises (`claude-code`), which leaves event names checked against no harness.
+
+Script reference rules:
+
+- Script references are read with apm 0.28.0's own patterns: `${PLUGIN_ROOT}/…` only when the path follows the token directly, up to the first whitespace or quote, and `./…` anywhere in the command.
+- A `./` or `../` match is held to the script rules — a FAIL when missing — only in command position, when it ends in a script extension, or when it names a package entry that is not a file; any other match (`npx prettier --check ./src`, `printf '.\n'`) is at most a SUGGESTION, because apm only warns and it runs against the consumer's working directory as meant.
+- Command position is the first token past any `NAME=value` assignments and `env` with its options, or the first operand after `bash`, `sh`, `zsh`, `python`, `python3`, `node`, `pwsh`, `ruby` or `perl`, past its options such as `-e` or `-u`; after a `sh`-family `-c`, the first token of the command string; inline code such as `python3 -c` has none. Absolute and bare relative script paths are checked in the same positions.
+- The exec bit is required of a script that runs directly: the first token, or the first token of a `-c` command string (`bash -c "${PLUGIN_ROOT}/x.sh"`). Through an interpreter it is not.
+- Each event is judged per target the package root's `apm.yml` deploys to — no `target:`/`targets:`, `all`, or no `apm.yml` means every hook target — after apm's rename map for that target: it FAILs when a target with a published event list (Claude, Copilot) does not fire the renamed name, whatever its casing.
+
+Exit codes: **0** with no FAIL, **1** on real findings, **2** when it never ran, including a crash inside the checks — report that as `### Structure` unverified, quoting the stderr reason. An INFO line is observational: report it under `### Structure` and count it in `· P info`.
+
+The command parser is a heuristic, not a shell. Known blind spots: a script after `&&`, `;` or a pipe inside one command, `env -S`, command substitution, and a quoted `-c` string that ends before the script are not in command position, so a bad reference there is at most a SUGGESTION or unseen. Read every command in Step 2 rather than taking a clean script run as proof.
 
 There is no provenance and no Vale step: a hook carries no `source_keys` and no prose.
 
-Five tiers deliberately differ from `primitive-author`'s checklist or the research's. Do not re-tier them by judgment:
+Six tiers deliberately differ from `primitive-author`'s checklist or the research's. Do not re-tier them by judgment:
 
-- A hook file directly under a package-root `hooks/` — beside the package's `apm.yml`, or beside a `plugin.json` at any location apm's `find_plugin_json` reads (root, `.github/plugin/`, `.claude-plugin/`, `.cursor-plugin/`) — passes. apm discovers both `.apm/hooks/` and `hooks/`, installs a Claude plugin with no `apm.yml`, and this audit may target a third-party package; `primitive-author` authors only in `.apm/hooks/`. Any other `hooks/` directory (`.github/hooks/`, `.cursor/hooks/`, …) is apm's deployed output and FAILs.
+- A hook file directly under a package-root `hooks/` — beside the package's `apm.yml`, or beside a `plugin.json` at any location apm's `find_plugin_json` reads (root, `.github/plugin/`, `.claude-plugin/`, `.cursor-plugin/`) — passes. apm discovers both `.apm/hooks/` and `hooks/`, installs a Claude plugin with no `apm.yml`, and this audit may target a third-party package; `primitive-author` authors only in `.apm/hooks/`. Any other `hooks/` directory (`.github/hooks/`, `.cursor/hooks/`, …) is apm's deployed output, or no package source at all, and FAILs at exit 1.
 - An event that every listed target fires, but that reaches a target with no published event list (Cursor, Kiro, Gemini, Codex, Antigravity, Windsurf) in a non-PascalCase form after apm's rename, is a SUGGESTION, not the FAIL Must 4 implies: the script cannot tell a harness's native spelling (Cursor's `stop`, Windsurf's `pre_run_command`) from a typo. A Cursor-only `stop` therefore exits 0.
 - Copilot counts every name apm's own Copilot map emits as fired (`userPromptSubmit`, although Copilot documents `userPromptSubmitted`): the author cannot route around apm's rename, so that is not a finding in the file.
 - Deprecated filename routing is a SUGGESTION, matching the author's Should: the research allows it when deprecated routing is intended.
-- A non-executable script run as the command's first token is a FAIL, stricter than the research's Should, because it fails every time it fires.
+- A non-executable script run directly (the first token, or first in a `-c` string) is a FAIL, stricter than the research's Should, because it fails every time it fires.
+- `primitive-author` hook Must 5 bans an absolute or bare relative path "in any position"; this audit checks command positions only, because a later argument is data the script cannot tell from a path. Judge the rest by reading in Step 3.
 
 ## Step 2 — Read the hook and its scripts