fix: verify tracked setup writes with the check-ignore + ls-files pair

plugins/ai-slop/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "ai-slop",
-  "version": "0.3.9",
+  "version": "0.3.10",
   "description": "Detects and removes AI-writing tells (slop) in checked-in markdown prose: em dashes, emoji formatting, AI vocabulary, negative parallelisms, chatbot phrases, filler, stacked hedging, citation artifacts, and the rest of a catalog distilled from Wikipedia's Signs of AI writing. Read-only audit by default with a deterministic detector plus a judgment rubric; an explicit fix action rewrites findings behind a semantic-diff guard. Findings conform to the detector-findings convention so the review fanout fix relay can consume them.",
   "author": {
     "name": "Melodic Software",

plugins/ai-slop/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.3.10]
+
+### Changed
+
+- `setup` verifies tracked config writes with the check-ignore + ls-files pair and reports written-but-untracked instead of success (#3584, customization-consistency Phase 1c).
+
 ## [0.3.9]
 
 - **Three directory-expansion defects survived 0.3.8.** A tracked file

plugins/ai-slop/skills/setup/SKILL.md

@@ -44,4 +44,8 @@ Everything `check` does, then the confirmed write:
 2. Write ONLY the team layer (`.claude/ai-slop.json`), showing the diff and getting explicit
    confirmation before writing. Never write the user-global or overlay layers on the user's
    behalf; name them as options the user edits themselves.
-3. Re-run `--show-config` and report the new effective state.
+3. Re-run `--show-config` and report the new effective state. Then run the tracked-file pair on
+   the written team file: `git check-ignore -v .claude/ai-slop.json` reports no match (a match is
+   FAIL with the pattern) AND `git ls-files --error-unmatch .claude/ai-slop.json` exits 0
+   (non-zero right after a fresh write means "written but untracked: commit it to share with the
+   team", never success).

plugins/claude-config/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "claude-config",
-  "version": "0.40.2",
+  "version": "0.40.3",
   "description": "Nine configuration-health skills (plus setup) for a repo's Claude Code configuration: audit (settings.json / .mcp.json / hooks / plugins / permissions drift), audit-automation-gaps (evidence-gated verdicts on automation gaps), audit-permission-grants (allow-rule / allowed-tools grants for auto-mode durability and portability), audit-permission-state (the permission rules actually in effect — every settings scope merged with per-rule provenance, what auto mode drops on entry, config written where nothing reads it, and which managed intents are enforced versus loosenable), draft-auto-mode-rules (interview and draft a paste-ready autoMode classifier block; prints only, never writes), audit-instructions (locally-owned instruction surfaces vs current model capability — proposes removals/rewrites of instructions the model no longer needs, and detects cross-surface instruction conflicts), audit-prompting-postures (the additive lane — posture guidance the prompting guide says a component's purpose needs but the component does not carry), audit-pass (one coordinated, ordered, resumable pass over a named target — three-scope inventory, run-time-derived exclusion set, stable finding identity, suppression memory, resume, one human gate — delegating every check to the plugin that owns it), and unhobble (the empirical bare-baseline experiment: reversibly strip a repo's standing instructions, log real stumbles against the current model, re-add only what evidence earns).",
   "author": {
     "name": "Melodic Software",

plugins/claude-config/CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to the `claude-config` plugin are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); this plugin uses semantic versioning.
 
+## [0.40.3]
+
+### Changed
+
+- `setup` verifies tracked config writes with the check-ignore + ls-files pair and reports written-but-untracked instead of success (#3584, customization-consistency Phase 1c).
+
 ## [0.40.2]
 
 ### Fixed

plugins/claude-config/skills/setup/SKILL.md

@@ -76,7 +76,9 @@ nested worktree the skill was invoked from, then report one row per layer. The s
 tracked/ignored question has opposite correct answers per layer, so verify each on its own terms:
 
 - **user-global** `~/.claude/audit-pass.md`: outside the worktree; no git command applies. INFO only.
-- **team** `.claude/audit-pass.md`: must be tracked. Untracked while present is a hard STOP:
+- **team** `.claude/audit-pass.md`: must be tracked, probed as the pair —
+  `git check-ignore -v` reports no match (a match is FAIL with the pattern) AND
+  `git ls-files --error-unmatch` exits 0. Untracked while present is a hard STOP:
   teammates never receive the shared suppressions.
 - **local overlay** `.claude/audit-pass.local.md`: must be gitignored and never staged. Staged or
   tracked is a FAIL: a personal deviation can reach team history.

plugins/code-tidying/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "code-tidying",
-  "version": "0.14.5",
+  "version": "0.14.6",
   "description": "Code tidying and comment hygiene: /code-tidying:tidy proactively hunts a rotated, glob-scoped lane for Beck-style tidyings under a research-backed scope budget and ships one tight PR; /code-tidying:batch-simplify sweeps a time window, a branch, or an entire repository through grouped, dependency-ordered simplification waves with a never-drop deferred-items contract; /code-tidying:dissolve-comments enforces self-describing expressive code over a diff or target, widening to the branch diff and then the whole repository when the tree is clean — deletes zero-information comments, dissolves code-expressible ones into names and structure behind a tests gate (safe mode restricts applied edits to removals), and keeps only terse load-bearing comments code cannot express; /code-tidying:audit-comment-residue is a read-only classifier that flags history, plan, conversational, and ticket/PR residue in code comments for author-applied deletion; /code-tidying:audit-dead-code is a read-only whole-repo dead-code hunter running four labelled lanes of unequal confidence (knip for TS/JS, vulture for Python, gopls for Go, and a portable grep lane for shell and other symbol languages), adjudicating every candidate against dynamic-usage evidence into a dead, uncertain, or alive verdict. Project-specific tidy lanes are scaffolded into a tracked .claude/tidy-lanes/ config folder by a re-runnable setup skill.",
   "author": {
     "name": "Melodic Software",

plugins/code-tidying/CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to the `code-tidying` plugin are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); this plugin uses semantic versioning.
 
+## [0.14.6]
+
+### Changed
+
+- `setup` verifies tracked config writes with the check-ignore + ls-files pair and reports written-but-untracked instead of success (#3584, customization-consistency Phase 1c).
+
 ## [0.14.5]
 
 ### Changed

plugins/code-tidying/skills/setup/SKILL.md

@@ -58,10 +58,13 @@ FAIL. Modify nothing, and do NOT run a tidy sweep. That is `/code-tidying:tidy`.
    headings. Unkeyed entries name no language to replace. Framing prose above the first `###` is fine.
 3. **No unreplaced placeholders**, a lane still containing a template `<placeholder>` resolves to a
    broken scope glob or watch-for pattern; FAIL, naming the file and the leftover token.
-4. **Tracked, not ignored**. Run `git check-ignore -v <file>` per lane file. A non-empty result means a
-   `.gitignore` pattern excludes that lane; these lanes are team-shared and take effect only when
-   committed, so an ignored lane is FAIL with the matching pattern in the remediation line (a directory
-   can be tracked while a pattern excludes an individual `.md` inside it).
+4. **Tracked, not ignored**. Per lane file, run both halves of the tracked-file pair:
+   `git check-ignore -v <file>` (a non-empty result means a `.gitignore` pattern excludes that lane;
+   FAIL with the matching pattern in the remediation line — a directory can be tracked while a
+   pattern excludes an individual `.md` inside it) AND `git ls-files --error-unmatch <file>`
+   (non-zero exit means the lane is un-ignored but untracked: report it — "commit it to share with
+   the team", downgraded to INFO only when the user confirms it is a deliberately private,
+   uncommitted lane per the declared deviation below).
 5. **Bundled lanes and templates**. INFO: report the bundled lanes and templates available as scaffold
    sources, so the reader knows what `apply` can generate.
 
@@ -115,10 +118,13 @@ only where a lane's scope genuinely needs the user's call.
 5. **Write the lane files.** Materialize each accepted lane at `.claude/tidy-lanes/<lane>.md`. Write only
    lanes the user confirmed; produce no empty scaffolds.
 6. **Verify after remediation.** Re-run the `check` probes on each written file, required sections
-   present, no leftover placeholder, and (per file) `git check-ignore -v <file>` confirms it is tracked,
-   not ignored. A non-empty `check-ignore` result means a `.gitignore` pattern excludes that lane; surface
-   the matching pattern and offer to fix `.gitignore` before reporting success, since these lanes are
-   team-shared and must be committed to take effect. `/code-tidying:tidy` resolves a lane only from
+   present, no leftover placeholder, and (per file) both halves of the tracked-file pair:
+   `git check-ignore -v <file>` reports no match (a non-empty result means a `.gitignore` pattern
+   excludes that lane; surface the matching pattern and offer to fix `.gitignore` before reporting
+   success) AND `git ls-files --error-unmatch <file>` exits 0 (non-zero means un-ignored but still
+   untracked, the guaranteed state right after a fresh write, so report "written but untracked:
+   commit it to share with the team", never success), since these lanes are team-shared and must
+   be committed to take effect. `/code-tidying:tidy` resolves a lane only from
    `.claude/tidy-lanes/<lane>.md` (then the bundled lane of that name), and its catalog lists
    `.claude/tidy-lanes/*.md`. There is no user-global or `*.local.*` overlay resolution (declared
    deviation per the config-cascade contract, #723). Every scaffolded lane is a tracked, team-shared file;

plugins/codebase-health/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "codebase-health",
-  "version": "0.8.4",
+  "version": "0.8.5",
   "description": "Repo-wide drift audit between docs, config, code, and architecture: verifies every factual claim against reality via parallel subagent fan-out, severity-rates findings, and reports read-only, delegating remediation to the implementation/verification lanes. Audit dimensions are configurable through a tracked .claude/codebase-health.md config file written by the setup skill.",
   "author": {
     "name": "Melodic Software",

plugins/codebase-health/CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to the `codebase-health` plugin are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); this plugin uses semantic versioning.
 
+## [0.8.5]
+
+### Changed
+
+- `setup` verifies tracked config writes with the check-ignore + ls-files pair and reports written-but-untracked instead of success (#3584, customization-consistency Phase 1c).
+
 ## [0.8.4]
 
 ### Changed

plugins/codebase-health/skills/setup/SKILL.md

@@ -88,9 +88,12 @@ the repo make the values unambiguous; ask only where a dimension's targets genui
    [`${CLAUDE_PLUGIN_ROOT}/skills/setup/templates/config-template.md`](templates/config-template.md) (replace every placeholder comment
    with real values; drop unused placeholder rows).
 6. **Verify after remediation.** Re-run the `check` probes on the written file. Dimension source lists
-   parse and name real paths, and `git check-ignore -v .claude/codebase-health.md` confirms it is
-   tracked, not ignored (surface the matching pattern and offer to fix `.gitignore` before reporting
-   success). Then **offer the overlay convention**: personal overrides go in
+   parse and name real paths, and both halves of the tracked-file pair hold:
+   `git check-ignore -v .claude/codebase-health.md` reports no match (a match is FAIL; surface the
+   pattern and offer to fix `.gitignore` before reporting success) AND
+   `git ls-files --error-unmatch .claude/codebase-health.md` exits 0 (non-zero means un-ignored but
+   still untracked, the guaranteed state right after a fresh write, so report "written but
+   untracked: commit it to share with the team", never success). Then **offer the overlay convention**: personal overrides go in
    `.claude/codebase-health.local.md`; recommend the consumer add the recursive `.claude/**/*.local.*`
    line to `.gitignore` if not already covered. A user-global base at `~/.claude/codebase-health.md` is also honored. Layers
    resolve user-global → team → local overlay, additively.

plugins/discovery/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "discovery",
-  "version": "0.16.5",
+  "version": "0.16.6",
   "description": "Structured discovery before changes: explore the local codebase, run disciplined multi-source external research, and reconstruct why a past decision was made from evidence outside the code — each dispatching a purpose-built subagent by default so the reading stays out of the main conversation, with source tiers, falsification, recency gates, an intent-evidence tier, and a corpus-coverage ledger — persisting EXPLORE.md / RESEARCH.md / INTENT.md index-plus-sidecar handoff artifacts.",
   "author": {
     "name": "Melodic Software",

plugins/discovery/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog — discovery plugin
 
+## [0.16.6]
+
+### Changed
+
+- `setup` verifies tracked config writes with the check-ignore + ls-files pair and reports written-but-untracked instead of success (#3584, customization-consistency Phase 1c).
+
 ## [0.16.5]
 
 ### Fixed

plugins/discovery/skills/setup/SKILL.md

@@ -109,7 +109,10 @@ reports "already configured".
    schema's `type: object`). Verify-or-create the memory root's self-ignoring `.gitignore` (announce the
    creation). **Never edit the consumer's root `.gitignore`.**
 3. **Verify.** Re-read `.claude/topic-docs.yaml` and report its effective values, never claim
-   persisted on the write alone.
+   persisted on the write alone. Then run the tracked-file pair on it: `git check-ignore -v`
+   reports no match (a match is FAIL with the pattern) AND `git ls-files --error-unmatch` exits 0
+   (non-zero right after a fresh write means "written but untracked: commit it to share with the
+   team", never success).
 
 ## Output
 

plugins/github/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "github",
-  "version": "0.3.5",
+  "version": "0.3.6",
   "description": "GitHub admin-plane audit, advice, and guided setup over the authenticated user's own gh CLI: billing and cost control, security posture, rulesets and settings drift, Actions policy, and every other org/repo/enterprise settings area. Grounded in live state and current official GitHub docs (zero vendored knowledge); read-only by default, every mutation user-in-loop.",
   "author": {
     "name": "Melodic Software",

plugins/github/CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to the `github` plugin are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); this plugin uses semantic versioning.
 
+## [0.3.6]
+
+### Changed
+
+- `setup` verifies tracked config writes with the check-ignore + ls-files pair and reports written-but-untracked instead of success (#3584, customization-consistency Phase 1c).
+
 ## [0.3.5]
 
 ### Changed

plugins/github/skills/setup/SKILL.md

@@ -30,7 +30,7 @@ config). No action given: run `check`, then offer `apply` if anything is missing
    | Layer | Verdict to check |
    |---|---|
    | user-global | exists / absent. No git verdict applies outside the worktree |
-   | team | must be tracked in git; untracked team config is a hard finding |
+   | team | must be tracked in git, probed as the pair (`git check-ignore -v` no match AND `git ls-files --error-unmatch` exit 0); untracked team config is a hard finding |
    | local overlay | must be gitignored and never staged |
 
    All three layers absent is a **valid state**, reported as "unconfigured: routing resolves to
@@ -72,6 +72,10 @@ config). No action given: run `check`, then offer `apply` if anything is missing
      never overwrite or append to a consumer's existing conventions.
 4. **Idempotency check**: when the merged answers equal the existing config, report "no changes
    needed" and write nothing. A second run with the same answers must produce zero file changes.
+   After a team-layer write, re-run the tracked-file pair on each written path
+   (`git check-ignore -v` no match AND `git ls-files --error-unmatch` exit 0); non-zero `ls-files`
+   right after a fresh write means "written but untracked: commit it to share with the team",
+   never success.
 5. **Recommend** the recursive gitignore line (`.claude/**/*.local.*`) if the consumer's
    `.gitignore` lacks it. The edit is theirs to make.
 

plugins/planning/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "planning",
-  "version": "0.34.4",
+  "version": "0.34.5",
   "userConfig": {
     "use_ask_user_question": {
       "type": "boolean",

plugins/planning/CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to the `planning` plugin are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); this plugin uses semantic versioning.
 
+## [0.34.5]
+
+### Changed
+
+- `setup` verifies tracked config writes with the check-ignore + ls-files pair and reports written-but-untracked instead of success (#3584, customization-consistency Phase 1c).
+
 ## [0.34.4]
 
 ### Changed

plugins/planning/skills/setup/SKILL.md

@@ -91,7 +91,10 @@ writes. Every bootstrap write is user-accepted.
    the user chose. Absent keys mean the documented defaults, so an all-defaults answer may
    yield a file with `contract_tier: branch` alone or the schema-valid empty mapping `{}`
    (optionally followed by comments), never a comment-only document, which YAML parses as null.
-   Preserve every schema key an existing file carries.
+   Preserve every schema key an existing file carries. After the write, run the tracked-file pair
+   on it: `git check-ignore -v` reports no match (a match is FAIL with the pattern) AND
+   `git ls-files --error-unmatch` exits 0 (non-zero right after a fresh write means "written but
+   untracked: commit it to share with the team", never success).
 
 ### Second concern. Standards bootstrap
 
@@ -111,6 +114,10 @@ implement it by reference, do not restate it. Plugin-side notes only:
   its `standards-contract` frontmatter at the binding's version, and the setup-owned
   `<standards_dir>/.gitignore` containing `*.local.md` (the personal-overlay ignore). Write
   `.claude/standards.yaml` only when the user relocates the root from the documented default.
+  After a bootstrap write, run the tracked-file pair on each written team file:
+  `git check-ignore -v` reports no match (a match is FAIL with the pattern) AND
+  `git ls-files --error-unmatch` exits 0 (non-zero right after a fresh write means "written but
+  untracked: commit it to share with the team", never success).
 - **Optional offers, never demands:** pointer-rule generation for indexed ecosystem surfaces
   (interactive only), and reorganizing mixed or spread standards content toward the SRP + index
   shape.

plugins/repo-fleet-hygiene/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "repo-fleet-hygiene",
-  "version": "0.23.10",
+  "version": "0.23.11",
   "description": "Cross-repository Git/GitHub fleet discovery, evidence rollup, and a gated apply verb that executes a prior fleet action plan behind one confirmation. Audit stays read-only and confidence-tiered; apply mutates only with --apply plus interactive confirmation or --yes.",
   "author": {
     "name": "Melodic Software",

plugins/repo-fleet-hygiene/CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to `repo-fleet-hygiene` are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); this plugin uses semantic versioning.
 
+## [0.23.11]
+
+### Changed
+
+- `setup` verifies tracked config writes with the check-ignore + ls-files pair and reports written-but-untracked instead of success (#3584, customization-consistency Phase 1c).
+
 ## [0.23.10]
 
 ### Changed