@codyswann/lisa 2.351.0 → 2.352.0

package/dist/opencode/plugin-templates/lisa-block-instruction-file-edits.ts

@@ -56,7 +56,7 @@ const LisaBlockInstructionFileEdits = async () => {
           "1. Every agent needs it every session, only in this project? That is a",
           "   project rule — capture it with /lisa:persist-learning so it lands in",
           "   the learnings ledger. The gardener (/lisa:learnings:audit) proposes",
-          "   promotion into .claude/rules/PROJECT_RULES.md as a human-gated ticket.",
+          "   promotion into the host-rules directory .agents/rules/ as a human-gated ticket.",
           "2. It changes how an existing skill behaves? Edit that skill's SKILL.md.",
           "3. It is true beyond this project? Propose it upstream via",
           "   /lisa:cross-pollinate, or open an issue on CodySwannGT/lisa.",

package/dist/strategies/copy-overwrite.d.ts

@@ -21,12 +21,19 @@ export declare class CopyOverwriteStrategy implements ICopyStrategy {
     /**
      * Resolve a differing managed file on a non-interactive apply.
      *
-     * There is no prompt available here, so the file is left alone and reported
-     * as `stale` — unless `--refresh-templates` covers it, which is the operator
-     * deciding in advance to take upstream's version. That flag is the supported
-     * way to deliver a changed enforcement guard to an installed project; without
-     * it the only route is deleting the file so the create path picks it up,
-     * which is a workaround nobody should have to know.
+     * There is no prompt available here, so a file the project may have
+     * customised is left alone and reported as `stale` — unless
+     * `--refresh-templates` covers it, which is the operator deciding in advance
+     * to take upstream's version.
+     *
+     * Lisa's own artifacts are not in that category and never wait for the flag.
+     * A version bump is how the fleet takes an upgrade, and it passes no flags, so
+     * gating `scripts/lisa-hooks/*` behind one meant a released security fix
+     * reached nobody: the fail-open fixes in #2374 shipped while installed repos
+     * kept running the vulnerable guard, until someone deleted the files by hand
+     * so the create path would recreate them. Lisa owns those files outright —
+     * see `isLisaOwnedTemplate` — so they refresh here, backed up first, and a
+     * project that wants to keep its own copy says so in `.lisaignore`.
      * @param sourcePath - Packaged template path
      * @param destPath - Installed file path
      * @param relativePath - Repo-relative path for reporting

package/dist/strategies/copy-overwrite.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"copy-overwrite.d.ts","sourceRoot":"","sources":["../../src/strategies/copy-overwrite.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAE7D,OAAO,KAAK,EAAE,aAAa,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAG9E;;;;;;GAMG;AACH,qBAAa,qBAAsB,YAAW,aAAa;IACzD,QAAQ,CAAC,IAAI,EAAG,gBAAgB,CAAU;IAE1C;;;;;;;OAOG;IACG,KAAK,CACT,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,MAAM,EAChB,YAAY,EAAE,MAAM,EACpB,OAAO,EAAE,eAAe,GACvB,OAAO,CAAC,mBAAmB,CAAC;IAuD/B;;;;;;;;;;;;;;;;;;;;;OAqBG;YACW,mBAAmB;CAuBlC"}

package/dist/strategies/copy-overwrite.js

@@ -1,6 +1,7 @@
 import * as fse from "fs-extra";
 import { copyFile } from "node:fs/promises";
 import { mayRefreshTemplate } from "../core/config.js";
+import { isLisaOwnedTemplate } from "../core/lisa-owned-templates.js";
 import { filesIdentical, ensureParentDir } from "../utils/file-operations.js";
 /**
  * Copy-overwrite strategy: Replace file if exists (prompts on conflict)
@@ -60,12 +61,19 @@ export class CopyOverwriteStrategy {
     /**
      * Resolve a differing managed file on a non-interactive apply.
      *
-     * There is no prompt available here, so the file is left alone and reported
-     * as `stale` — unless `--refresh-templates` covers it, which is the operator
-     * deciding in advance to take upstream's version. That flag is the supported
-     * way to deliver a changed enforcement guard to an installed project; without
-     * it the only route is deleting the file so the create path picks it up,
-     * which is a workaround nobody should have to know.
+     * There is no prompt available here, so a file the project may have
+     * customised is left alone and reported as `stale` — unless
+     * `--refresh-templates` covers it, which is the operator deciding in advance
+     * to take upstream's version.
+     *
+     * Lisa's own artifacts are not in that category and never wait for the flag.
+     * A version bump is how the fleet takes an upgrade, and it passes no flags, so
+     * gating `scripts/lisa-hooks/*` behind one meant a released security fix
+     * reached nobody: the fail-open fixes in #2374 shipped while installed repos
+     * kept running the vulnerable guard, until someone deleted the files by hand
+     * so the create path would recreate them. Lisa owns those files outright —
+     * see `isLisaOwnedTemplate` — so they refresh here, backed up first, and a
+     * project that wants to keep its own copy says so in `.lisaignore`.
      * @param sourcePath - Packaged template path
      * @param destPath - Installed file path
      * @param relativePath - Repo-relative path for reporting
@@ -74,7 +82,8 @@ export class CopyOverwriteStrategy {
      */
     async applyNonInteractive(sourcePath, destPath, relativePath, context) {
         const { config, backupFile } = context;
-        if (!mayRefreshTemplate(relativePath, config.refreshTemplates)) {
+        if (!isLisaOwnedTemplate(relativePath) &&
+            !mayRefreshTemplate(relativePath, config.refreshTemplates)) {
             return { relativePath, strategy: this.name, action: "stale" };
         }
         // Backed up first: opting in to an overwrite is not opting out of being

package/dist/strategies/copy-overwrite.js.map

@@ -1 +1 @@
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package/dist/sync/registry.d.ts.map

@@ -1 +1 @@
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package/dist/sync/registry.js

@@ -10,7 +10,6 @@
  * completely missing.
  * @module sync/registry
  */
-import { DEFAULT_PROJECT_RULES_FILE } from "../core/project-config.js";
 import { validateHealthSchedule } from "../health/contract.js";
 import { BUILD_LABEL_DEFAULTS, LINEAR_WORKFLOW_DEFAULTS, PRD_LABEL_DEFAULTS, } from "./lifecycle-defaults.js";
 const WHEN_TRACKER_JIRA = "tracker=jira";
@@ -73,11 +72,6 @@ export const SYNC_REGISTRY = [
         defaultValue: "claude",
         description: "Target coding-agent harness(es)",
     },
-    {
-        key: "projectRulesFile",
-        defaultValue: DEFAULT_PROJECT_RULES_FILE,
-        description: "Hand-authored project rules file (independent of the ledger)",
-    },
     {
         key: "health.schedule",
         defaultValue: "off",

package/dist/sync/registry.js.map

@@ -1 +1 @@
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package/package.json

@@ -120,7 +120,7 @@
     }
   },
   "name": "@codyswann/lisa",
-  "version": "2.351.0",
+  "version": "2.352.0",
   "description": "Claude Code governance framework that applies guardrails, guidance, and automated enforcement to projects",
   "main": "dist/index.js",
   "exports": {

package/plugins/lisa/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa",
-  "version": "2.351.0",
+  "version": "2.352.0",
   "description": "Universal governance — agents, skills, commands, hooks, and rules for all projects",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa",
-  "version": "2.351.0",
+  "version": "2.352.0",
   "description": "Universal governance: agents, skills, commands, hooks, and rules for all projects.",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa/.codex-plugin/skills/lisa-debrief/SKILL.md

@@ -72,7 +72,7 @@ A markdown triage document at `./debrief/<initiative-slug>-<YYYY-MM-DD>.md` (or
    - `Summary` — one sentence
    - `Category`
    - `Evidence` — links to the source ticket comment / PR comment / commit / test file (multiple allowed)
-   - `Recommended persistence destination` — the agent's best guess for where this should land if accepted (e.g., "Edge Case Brainstorm checklist → Navigation & URL state", "learnings ledger via the executable contract", "new tooling-gap ticket", "upstream Lisa issue"). Never name machine-local auto-memory, `PROJECT_RULES.md`, or `AGENTS.md` — those are not persistence destinations.
+   - `Recommended persistence destination` — the agent's best guess for where this should land if accepted (e.g., "Edge Case Brainstorm checklist → Navigation & URL state", "learnings ledger via the executable contract", "new tooling-gap ticket", "upstream Lisa issue"). Never name machine-local auto-memory, the host-rules directory `.agents/rules/`, or `AGENTS.md` — those are not persistence destinations.
    - `Disposition` — empty checkbox-style field the human will fill: `[ ] Accept` / `[ ] Reject` / `[ ] Defer` plus a free-text reason
 4. **Source map** — appendix listing every work item and PR walked, so the human can verify completeness.
 

package/plugins/lisa/.codex-plugin/skills/lisa-debrief-apply/SKILL.md

@@ -18,7 +18,7 @@ A path or URL to a Debrief triage document produced by `lisa-debrief`. The docum
 
 1. **Verify the doc exists and parses.** If the file cannot be read or the expected sections are missing, stop and report — do not guess.
 2. **Confirm dispositions exist.** If every row is unmarked, stop and ask the human to triage first. A pristine doc is a no-op, not an error to silently swallow.
-3. **Identify the destination map.** Read the project's `.lisa.config.json` (or stack defaults) for: edge-case checklist file (default: `plugins/src/base/rules/intent-routing.md`'s Edge Case Brainstorm sub-flow), the committed learnings ledger path (resolve it — never hardcode — via `resolveProjectLearningsFile` from `@codyswann/lisa/learnings`: the `learnings.file` override, else the default `.lisa/PROJECT_LEARNINGS.md`), tracker for new tickets. The three knowledge categories (recurring gotcha, process friction, convention drift) all land in the ledger now; machine-local auto-memory and `PROJECT_RULES.md` / `AGENTS.md` are no longer knowledge destinations (see [Ledger persistence](#ledger-persistence-knowledge-categories)).
+3. **Identify the destination map.** Read the project's `.lisa.config.json` (or stack defaults) for: edge-case checklist file (default: `plugins/src/base/rules/intent-routing.md`'s Edge Case Brainstorm sub-flow), the committed learnings ledger path (resolve it — never hardcode — via `resolveProjectLearningsFile` from `@codyswann/lisa/learnings`: the `learnings.file` override, else the default `.lisa/PROJECT_LEARNINGS.md`), tracker for new tickets. The three knowledge categories (recurring gotcha, process friction, convention drift) all land in the ledger now; machine-local auto-memory and host rules (`.agents/rules/`) / `AGENTS.md` are no longer knowledge destinations (see [Ledger persistence](#ledger-persistence-knowledge-categories)).
 
 ## Routing rules
 
@@ -61,13 +61,13 @@ For each such Accepted row:
    - `first_learned` = `last_confirmed` = today (ISO date; on consolidation keep the superseded entry's earliest `first_learned`).
    - `confidence` = **`high`**. A human marking the row **Accept** is corroboration — an independent human judgement that the learning is real — so a debrief-accepted entry starts higher than the learner's single-occurrence auto-capture (which defaults to `low`). The writer re-asserts the entry and token budgets; an over-budget failure means consolidate harder or drop, never truncate by hand.
 
-**Machine-local memory is no longer a knowledge destination.** Auto-memory (`project_*.md`, `MEMORY.md`) remains available only for the assistant's *personal* collaboration notes — it is invisible to cloud runs and to teammates, so it can never hold shared project knowledge. **`AGENTS.md` is human-authored** agent operating instruction — it is the source of truth, and `CLAUDE.md` is only a one-line `@AGENTS.md` pointer — and `PROJECT_RULES.md` is durable human-authored guidance; `apply` never writes to any of the three for these categories.
+**Machine-local memory is no longer a knowledge destination.** Auto-memory (`project_*.md`, `MEMORY.md`) remains available only for the assistant's *personal* collaboration notes — it is invisible to cloud runs and to teammates, so it can never hold shared project knowledge. **`AGENTS.md` is human-authored** agent operating instruction — it is the source of truth, and `CLAUDE.md` is only a one-line `@AGENTS.md` pointer — and the host-rules directory `.agents/rules/` is durable human-authored guidance; `apply` never writes to any of the three for these categories.
 
 ## Idempotency
 
 `apply` is safe to re-run. Each Accepted row carries an evidence link that doubles as a fingerprint. Before writing, check whether the destination already cites that fingerprint:
 
-- **Knowledge categories (gotcha, friction, drift) → ledger.** Parse the ledger once with `parseLearningsFile` from `@codyswann/lisa/learnings` and scan the entries' `provenance` for the row's evidence link. If any entry's provenance already contains it, the row is already persisted — skip the write. This replaces the old scattered-file greps (memory files, `PROJECT_RULES.md`, `AGENTS.md`): provenance in the single governed ledger is now the one fingerprint surface.
+- **Knowledge categories (gotcha, friction, drift) → ledger.** Parse the ledger once with `parseLearningsFile` from `@codyswann/lisa/learnings` and scan the entries' `provenance` for the row's evidence link. If any entry's provenance already contains it, the row is already persisted — skip the write. This replaces the old scattered-file greps (memory files, host rules, `AGENTS.md`): provenance in the single governed ledger is now the one fingerprint surface.
 - **Other categories** keep their existing destination check (the tracker for the ticket marker, the PRD for the defect comment, `intent-routing.md` for the edge-case citation).
 
 If the fingerprint is already present, skip the write and note the row as `already-applied` in the run summary. This lets the human triage a doc incrementally (mark a few, run apply, mark more, run apply again) without producing duplicates.

package/plugins/lisa/.codex-plugin/skills/lisa-doctor/SKILL.md

@@ -56,7 +56,10 @@ as applicable to the current repo:
    and `source` only. If a required CLI, MCP surface, or auth context is unavailable in the current
    runtime, report that explicitly instead of pretending the repo is ready.
 4. **Runtime distribution surfaces** — confirm the command, skill, hook, and related distribution
-   surfaces relevant to this repo are present where Lisa expects them on the active runtime.
+   surfaces relevant to this repo are present where Lisa expects them on the active runtime, and
+   that the Lisa-owned enforcement artifacts (`scripts/lisa-hooks/*`,
+   `scripts/lisa-enforcement-fallback.sh`) match the installed Lisa version rather than an older
+   copy. Present-but-stale is a finding: a guard whose fix never landed enforces the old behavior.
 5. **Automation readiness** — inspect whether the configured queue source/tracker and scheduling
    prerequisites are observable, but do **not** create, edit, or delete automations during doctor.
 6. **Optional GitHub Project coordination** — when `github.projects.v2` is configured, delegate

package/plugins/lisa/.codex-plugin/skills/lisa-improve-harness/SKILL.md

@@ -341,7 +341,7 @@ Any durable lesson the loop produced is **submitted** to `lisa-persist-learning`
 only write path per the `project-learnings` rule) as a candidate; its hostile-default judge — not
 this skill, and not the caller — decides the disposition. A dropped candidate is recorded in
 `Known limits`, never reported as routed or owned. This skill never writes the learnings file,
-`PROJECT_RULES.md`, or `CLAUDE.md` itself, and never promotes a learning to a higher rung (that
+host rules (`.agents/rules/`), or `CLAUDE.md` itself, and never promotes a learning to a higher rung (that
 is the gardener's ticket-gated job).
 
 ## Idempotency
@@ -483,5 +483,5 @@ its face, because a single-trajectory loop always has limits.
 - **Bounded claims.** One trajectory supports one trajectory's claim. No comparative,
   longitudinal, or population claims; `Known limits` is never empty.
 - **One write path for learnings.** Durable lessons are submitted to `lisa-persist-learning` for
-  judgment; this skill never edits the learnings ledger, `PROJECT_RULES.md`, or a rules tree,
+  judgment; this skill never edits the learnings ledger or any rules tree (host `.agents/rules/` included),
   and never promotes a learning to a higher rung.

package/plugins/lisa/.codex-plugin/skills/lisa-learnings-audit/SKILL.md

@@ -49,9 +49,12 @@ memorized list:
    — stronger than an omission count, because room was not merely tight, a real
    capture was turned away. Drain it every run (see The audit cycle).
 3. **Rules trees** — the plugin `rules/eager/` + `rules/reference/` pairs AND
-   the host project's `.claude/rules/` (e.g. `PROJECT_RULES.md`, which is
-   human-authored only — its existing sections are still audit candidates;
-   first-run candidates come from exactly there).
+   the host project's canonical host-rules directory `.agents/rules/`, plus any
+   retired-but-surviving single-file rules the project still carries
+   (`.claude/rules/PROJECT_RULES.md`, or a legacy `projectRulesFile` path).
+   All of it is human-authored only — the gardener proposes, it never rewrites —
+   and its existing sections are still audit candidates; first-run candidates
+   come from exactly there.
 4. **Skills** — `.claude/skills/` and the plugin skill roots the runtime
    exposes (descriptions are eager context; bodies load on invoke).
 5. **The wiki index** — `wiki/index.md` when the project has a wiki.

package/plugins/lisa/agents/learnings-synthesizer.md

@@ -44,7 +44,7 @@ Map every finding to exactly one category. When a finding could fit two, pick th
 
 A finding that does not fit any of the eight is itself a signal — surface it under an additional ad-hoc category `Uncategorized` with a note explaining why no category fit. Better to surface than to drop.
 
-The destination column is a **hint for the human triaging the row**, not the routing decision: `lisa-debrief-apply` routes on the category, never on this column. Keep the hint honest anyway — a human decides Accept/Reject partly on where the learning will land. The three knowledge categories (recurring gotcha, process friction, convention drift) all land in the committed learnings ledger through the executable contract. Machine-local auto-memory (`project_*.md`, `MEMORY.md`), `PROJECT_RULES.md`, and `AGENTS.md` (whose `CLAUDE.md` is only a `@AGENTS.md` pointer) are **never** destinations — the first is invisible to cloud runs and teammates, and the latter two are human-authored surfaces that agents do not write.
+The destination column is a **hint for the human triaging the row**, not the routing decision: `lisa-debrief-apply` routes on the category, never on this column. Keep the hint honest anyway — a human decides Accept/Reject partly on where the learning will land. The three knowledge categories (recurring gotcha, process friction, convention drift) all land in the committed learnings ledger through the executable contract. Machine-local auto-memory (`project_*.md`, `MEMORY.md`), the host-rules directory `.agents/rules/`, and `AGENTS.md` (whose `CLAUDE.md` is only a `@AGENTS.md` pointer) are **never** destinations — the first is invisible to cloud runs and teammates, and the latter two are human-authored surfaces that agents do not write.
 
 ## Dedupe rules
 

package/plugins/lisa/agents/skill-evaluator.md

@@ -18,7 +18,7 @@ Rungs are ordered by context cost and enforcement strength. Decision vocabulary:
 | Rung | Recommendation | Destination | Enters context | Admission policy |
 | --- | --- | --- | --- | --- |
 | 6 | EXECUTABLE-CONTROL | Lint / ast-grep / type / test / hook / `package.lisa.json` force | Never — diagnostic fires on violation | Mechanically decidable + stable + recurred |
-| 5 | EAGER-RULE | Auto-loaded rules tree | Unconditionally, every session | **Earned by failure evidence** (repeated misses despite retrievability); demotion-biased |
+| 5 | EAGER-RULE | Host rules: `.agents/rules/` (project scope) · plugin `rules/eager/` (upstream scope) | Unconditionally, every session | **Earned by failure evidence** (repeated misses despite retrievability); demotion-biased |
 | 4 | SKILL | `.claude/skills/<name>/SKILL.md` | Description eager; body on invoke | Procedural, complex, recognizable trigger |
 | 3 | WIKI | Wiki page + index entry | Only when routed to | Durable reference knowledge |
 | 2 | KEEP-IN-LEDGER | `PROJECT_LEARNINGS.md` (bounded contract projection) | Bounded projection only | Default landing zone; probationary, expiring |

package/plugins/lisa/hooks/block-instruction-file-edits.sh

@@ -117,7 +117,7 @@ WHERE IT GOES INSTEAD — take the first one that fits:
    That is a project rule — but do not write it yourself. Capture it with
    \`/lisa:persist-learning\` so it lands in the learnings ledger with provenance
    and a confidence score. The gardener (\`/lisa:learnings:audit\`) then proposes
-   promotion into \`.claude/rules/PROJECT_RULES.md\` as a human-gated ticket.
+   promotion into the host-rules directory \`.agents/rules/\` as a human-gated ticket.
 
 2. It changes how an existing skill should behave. Edit that skill's SKILL.md.
    Knowledge belongs next to the procedure it modifies, not in a global preamble.

package/plugins/lisa/hooks/block-shell-json-parsing.sh

@@ -3,7 +3,7 @@
 # Text tools (grep/sed/cut/awk) break on valid JSON — multiline values, escaped
 # quotes, reordered keys, nested objects — producing silently wrong output
 # instead of errors. jq is the required tool for structural JSON reads and
-# writes in shell. Promoted from PROJECT_RULES.md prose to an executable
+# writes in shell. Promoted from host-rules prose to an executable
 # control by the learnings gardener (issue #1787).
 #
 # Precision-first: this hook fires only on high-confidence STRUCTURAL parsing

package/plugins/lisa/rules/eager/config-resolution.md

@@ -37,9 +37,12 @@ This is the shared slug for the config-bound-transitions policy (the `leaf-only-
 
 ## Project rules and learnings
 
-Resolve hand-authored project rules from `.lisa.config.json`
-`projectRulesFile`, defaulting to `.claude/rules/PROJECT_RULES.md`. Automated
-learnings never append to that file: they use the separate machine-managed
+Host-authored project rules live in the fixed, agent-neutral directory
+`.agents/rules/` — not a configurable file. Every agent reaches it through the
+Lisa-managed pointer block in `AGENTS.md`, so it is read once, on demand. A
+project that still carries the retired `.claude/rules/PROJECT_RULES.md` keeps
+it, untouched and authoritative; the pointer names it too. Automated
+learnings never append to host rules: they use the separate machine-managed
 ledger resolved from `.lisa.config.json` — the optional `learnings.file`
 override, else the default `.lisa/PROJECT_LEARNINGS.md`. The ledger lives in the
 cold `.lisa/` tree (never an auto-loaded rules directory) and is consumed only

package/plugins/lisa/rules/eager/project-learnings.md

@@ -15,7 +15,8 @@ receive the contract's bounded projection, not the full file.
 
 Missing learnings are a silent no-op. Malformed, non-canonical, unsafe, or
 over-budget learnings produce one readable warning, apply no entry, and must not
-block unrelated task work. Never append automated learnings to
-`PROJECT_RULES.md`; project learnings are a separate machine-managed document.
+block unrelated task work. Never append automated learnings to host rules
+(`.agents/rules/`, or a surviving legacy `PROJECT_RULES.md`); project learnings
+are a separate machine-managed document.
 
 Full prose: [reference/project-learnings.md](../reference/project-learnings.md).

package/plugins/lisa/rules/reference/config-resolution.md

@@ -33,7 +33,6 @@ fi
 {
   "tracker": "jira",
   "source":  "notion",
-  "projectRulesFile": ".claude/rules/PROJECT_RULES.md",
 
   "atlassian":  { "cloudId": "<uuid>", "site": "<host>" },
   "jira": {
@@ -179,12 +178,21 @@ fi
 |-------|----------|---------|-------|
 | `tracker` | **yes** | — | Destination for ticket writes. One of `"jira"`, `"github"`, `"linear"`. Missing → fail with instruction to run the matching `/lisa:setup:*` skill. |
 | `source` | no | — | Default PRD source for batch skills (`/lisa:intake`) and arg-less single-PRD skills. One of `"notion"`, `"confluence"`, `"linear"`, `"github"`, `"jira"`. Explicit URLs/keys passed to a skill always win over `source`; this is a default, not a lock. |
-| `projectRulesFile` | no | `.claude/rules/PROJECT_RULES.md` | Safe repo-relative Markdown path for hand-authored project rules. Independent of the learnings ledger — relocating the rules file never moves the ledger. |
+| ~~`projectRulesFile`~~ | — | — | **Retired.** Host-authored rules now live in the fixed, agent-neutral directory `.agents/rules/` — not a configurable file. An existing key is still parsed and preserved so installed projects keep applying, but nothing serves rules from it. See **Host rules** below. |
 | `learnings.file` | no | `.lisa/PROJECT_LEARNINGS.md` | Safe repo-relative Markdown path for the machine-managed learnings ledger, overriding the `.lisa/` default. Rejected if it resolves inside any auto-loaded rules tree (`.claude/rules`, `.cursor/rules`, `.github/instructions`, `.agents/rules`) — the ledger must stay out of eager context. |
 | `health.schedule` | no | `off` | Health cadence contract: `off`, `daily`, or `weekly`. `lisa sync` populates the default with `_lisaSync.populated` provenance and rejects values outside this closed vocabulary. Runtime results live only at the gitignored `.lisa/health/latest.json`, never in either config file. |
 | `usage` | no | — | Optional token/cost pricing metadata consumed by the `usage-accounting` rule. Missing pricing never blocks a lifecycle flow; Lisa records token counts with `estimated_cost: null` when no trustworthy price source is configured. |
 | `wiki` | no | — | Wiki location for the `wiki-knowledge-source` rule. Omit for a local in-repo wiki (`wiki/`). See **Wiki source** below. |
 
+### Host rules (`.agents/rules/`)
+
+Host-authored operating rules live in `.agents/rules/` — **fixed, not configurable**. One directory, every agent.
+
+- **Not a native auto-load tree.** `.claude/rules`, `.cursor/rules`, and `.github/instructions` are; `.agents/rules` deliberately is not. Every agent reaches it through the single Lisa-managed pointer block in `AGENTS.md` (Claude via the `@AGENTS.md` import in `CLAUDE.md`), so no agent loads host rules twice.
+- **Host-owned.** Lisa never writes rule bodies into `.agents/rules/`, and never edits or deletes a file there. Lisa's own rules originate in its plugins and arrive by their own route.
+- **Not the learnings ledger.** `.agents/rules` is reserved in the auto-loaded-tree blocklist, so a `learnings.file` override can never resolve inside it.
+- **Transition.** A project that still has the retired `.claude/rules/PROJECT_RULES.md` keeps it, untouched and authoritative. The pointer block names it so agents whose runtime does not auto-load `.claude/rules/` still find it. Moving that content is a human-gated decision, never an automated rewrite.
+
 ### Wiki source (`wiki`)
 
 Declares **where this repo's LLM Wiki lives** so the query/ingest skills can resolve and (for a remote wiki) mirror it. `wiki.source` has two shapes — **local** (`path`) and **remote** (`url`) — and the block belongs in the **consumer** repo's `.lisa.config.json`, not in `wiki/lisa-wiki.config.json` (which describes a wiki from the inside and is unavailable until a remote wiki is mirrored — chicken-and-egg). The whole `wiki` block is optional; omit it and the resolver falls back to the in-repo `wiki/` convention.

package/plugins/lisa/rules/reference/intent-routing.md

@@ -223,7 +223,7 @@ Sequence:
    - **PRD defect** — the ticket faithfully captured the PRD, but the PRD itself was wrong, ambiguous, or missing the failing case
    - **Missing tool access** — an agent lacked a tool, credential, environment, or permission the work required
 
-   The three knowledge categories (recurring gotcha, process friction, convention drift) persist to the committed learnings ledger through the executable contract — never to machine-local memory, `PROJECT_RULES.md`, or `AGENTS.md`.
+   The three knowledge categories (recurring gotcha, process friction, convention drift) persist to the committed learnings ledger through the executable contract — never to machine-local memory, host rules (`.agents/rules/`), or `AGENTS.md`.
 4. **Produce the human-triage document** — a markdown file with one row per candidate learning showing: category, summary, evidence (links to the source ticket comment / PR comment / commit), recommended persistence destination, and a checkbox-style disposition field the human will mark (Accept / Reject / Defer). Surface step-1 anomalies (work items missing PRs, etc.) in a separate section. The document is exhaustive — it lists every candidate, even ones the synthesizer rates low confidence — because the human, not the agent, decides what is worth keeping.
 5. **Record Debrief usage on the triage document** — invoke `lisa-usage-accounting` against the generated markdown artifact so the document carries its own direct `debrief` usage entry in the canonical `## Lisa Usage` section. If runtime usage is unavailable, write the entry with `source: unavailable` and nullable token/cost fields rather than skipping it.
 6. **Stop and hand the document to the human.** Debrief does NOT persist accepted learnings itself. The human triages, marks dispositions, and runs the **`/lisa:debrief:apply`** command (skill: `debrief-apply`) to route the accepted items to their destinations.

package/plugins/lisa/rules/reference/project-learnings.md

@@ -34,7 +34,7 @@ Each persisted entry has seven fields:
 
 - The **learner agent** at capture time appends or consolidates new entries
   (`persistLearningEntry` / `persistConsolidatedLearning`) from task learnings.
-  It is capture-only: it never appends to `PROJECT_RULES.md`, creates skills, or
+  It is capture-only: it never appends to host rules, creates skills, or
   files upstream issues — promotion is the gardener's ticket-gated job.
 - **`lisa-debrief-apply`** routes accepted debrief findings in the three
   knowledge categories — recurring gotcha, process friction, convention drift —
@@ -42,7 +42,8 @@ Each persisted entry has seven fields:
   `persistConsolidatedLearning`, with consolidation-at-write), provenance drawn
   from the triage row's evidence links and a `high` starting confidence because
   a human Accept is corroboration. It no longer writes to machine-local memory,
-  `PROJECT_RULES.md`, or `AGENTS.md` (the human-authored source of truth, of
+  the host-rules directory `.agents/rules/` (or a surviving legacy
+  `PROJECT_RULES.md`), or `AGENTS.md` (the human-authored source of truth, of
   which `CLAUDE.md` is only a `@AGENTS.md` pointer) for these categories.
 - The **build-intake flows** advance `last_confirmed` at claim time
   (`confirmLearningEntry`, below).
@@ -77,9 +78,10 @@ warning, apply no entry, and do not block unrelated work.
 Precedence:
 
 1. System, developer, user, and repo instructions still outrank learnings.
-2. Committed project rules remain durable human-authored guidance.
+2. Committed host rules (`.agents/rules/`) remain durable human-authored
+   guidance.
 3. Project learnings add recent operational knowledge, but never rewrite or
-   append to `PROJECT_RULES.md`.
+   append to host rules.
 
 ## Task telemetry (MLD) is not context
 

package/plugins/lisa/rules/reference/promotion-contract.md

@@ -121,6 +121,7 @@ and lets reviewers diff against a single source of truth.
 - **The gardener** (`lisa-learnings-audit`): embeds the AC template above into
   EXECUTABLE-CONTROL promotion tickets and applies the eager-tier admission
   policy when auditing.
-- **PROJECT_RULES.md owners**: that file is human-authored only; machine
+- **Host-rules owners** (`.agents/rules/`, plus any surviving legacy
+  `PROJECT_RULES.md`): that surface is human-authored only; machine
   writes go to the learnings ledger, and promotions out of it arrive as
   gardener tickets governed by this contract.

package/plugins/lisa/skills/lisa-debrief/SKILL.md

@@ -72,7 +72,7 @@ A markdown triage document at `./debrief/<initiative-slug>-<YYYY-MM-DD>.md` (or
    - `Summary` — one sentence
    - `Category`
    - `Evidence` — links to the source ticket comment / PR comment / commit / test file (multiple allowed)
-   - `Recommended persistence destination` — the agent's best guess for where this should land if accepted (e.g., "Edge Case Brainstorm checklist → Navigation & URL state", "learnings ledger via the executable contract", "new tooling-gap ticket", "upstream Lisa issue"). Never name machine-local auto-memory, `PROJECT_RULES.md`, or `AGENTS.md` — those are not persistence destinations.
+   - `Recommended persistence destination` — the agent's best guess for where this should land if accepted (e.g., "Edge Case Brainstorm checklist → Navigation & URL state", "learnings ledger via the executable contract", "new tooling-gap ticket", "upstream Lisa issue"). Never name machine-local auto-memory, the host-rules directory `.agents/rules/`, or `AGENTS.md` — those are not persistence destinations.
    - `Disposition` — empty checkbox-style field the human will fill: `[ ] Accept` / `[ ] Reject` / `[ ] Defer` plus a free-text reason
 4. **Source map** — appendix listing every work item and PR walked, so the human can verify completeness.
 

package/plugins/lisa/skills/lisa-debrief-apply/SKILL.md

@@ -18,7 +18,7 @@ A path or URL to a Debrief triage document produced by `lisa-debrief`. The docum
 
 1. **Verify the doc exists and parses.** If the file cannot be read or the expected sections are missing, stop and report — do not guess.
 2. **Confirm dispositions exist.** If every row is unmarked, stop and ask the human to triage first. A pristine doc is a no-op, not an error to silently swallow.
-3. **Identify the destination map.** Read the project's `.lisa.config.json` (or stack defaults) for: edge-case checklist file (default: `plugins/src/base/rules/intent-routing.md`'s Edge Case Brainstorm sub-flow), the committed learnings ledger path (resolve it — never hardcode — via `resolveProjectLearningsFile` from `@codyswann/lisa/learnings`: the `learnings.file` override, else the default `.lisa/PROJECT_LEARNINGS.md`), tracker for new tickets. The three knowledge categories (recurring gotcha, process friction, convention drift) all land in the ledger now; machine-local auto-memory and `PROJECT_RULES.md` / `AGENTS.md` are no longer knowledge destinations (see [Ledger persistence](#ledger-persistence-knowledge-categories)).
+3. **Identify the destination map.** Read the project's `.lisa.config.json` (or stack defaults) for: edge-case checklist file (default: `plugins/src/base/rules/intent-routing.md`'s Edge Case Brainstorm sub-flow), the committed learnings ledger path (resolve it — never hardcode — via `resolveProjectLearningsFile` from `@codyswann/lisa/learnings`: the `learnings.file` override, else the default `.lisa/PROJECT_LEARNINGS.md`), tracker for new tickets. The three knowledge categories (recurring gotcha, process friction, convention drift) all land in the ledger now; machine-local auto-memory and host rules (`.agents/rules/`) / `AGENTS.md` are no longer knowledge destinations (see [Ledger persistence](#ledger-persistence-knowledge-categories)).
 
 ## Routing rules
 
@@ -61,13 +61,13 @@ For each such Accepted row:
    - `first_learned` = `last_confirmed` = today (ISO date; on consolidation keep the superseded entry's earliest `first_learned`).
    - `confidence` = **`high`**. A human marking the row **Accept** is corroboration — an independent human judgement that the learning is real — so a debrief-accepted entry starts higher than the learner's single-occurrence auto-capture (which defaults to `low`). The writer re-asserts the entry and token budgets; an over-budget failure means consolidate harder or drop, never truncate by hand.
 
-**Machine-local memory is no longer a knowledge destination.** Auto-memory (`project_*.md`, `MEMORY.md`) remains available only for the assistant's *personal* collaboration notes — it is invisible to cloud runs and to teammates, so it can never hold shared project knowledge. **`AGENTS.md` is human-authored** agent operating instruction — it is the source of truth, and `CLAUDE.md` is only a one-line `@AGENTS.md` pointer — and `PROJECT_RULES.md` is durable human-authored guidance; `apply` never writes to any of the three for these categories.
+**Machine-local memory is no longer a knowledge destination.** Auto-memory (`project_*.md`, `MEMORY.md`) remains available only for the assistant's *personal* collaboration notes — it is invisible to cloud runs and to teammates, so it can never hold shared project knowledge. **`AGENTS.md` is human-authored** agent operating instruction — it is the source of truth, and `CLAUDE.md` is only a one-line `@AGENTS.md` pointer — and the host-rules directory `.agents/rules/` is durable human-authored guidance; `apply` never writes to any of the three for these categories.
 
 ## Idempotency
 
 `apply` is safe to re-run. Each Accepted row carries an evidence link that doubles as a fingerprint. Before writing, check whether the destination already cites that fingerprint:
 
-- **Knowledge categories (gotcha, friction, drift) → ledger.** Parse the ledger once with `parseLearningsFile` from `@codyswann/lisa/learnings` and scan the entries' `provenance` for the row's evidence link. If any entry's provenance already contains it, the row is already persisted — skip the write. This replaces the old scattered-file greps (memory files, `PROJECT_RULES.md`, `AGENTS.md`): provenance in the single governed ledger is now the one fingerprint surface.
+- **Knowledge categories (gotcha, friction, drift) → ledger.** Parse the ledger once with `parseLearningsFile` from `@codyswann/lisa/learnings` and scan the entries' `provenance` for the row's evidence link. If any entry's provenance already contains it, the row is already persisted — skip the write. This replaces the old scattered-file greps (memory files, host rules, `AGENTS.md`): provenance in the single governed ledger is now the one fingerprint surface.
 - **Other categories** keep their existing destination check (the tracker for the ticket marker, the PRD for the defect comment, `intent-routing.md` for the edge-case citation).
 
 If the fingerprint is already present, skip the write and note the row as `already-applied` in the run summary. This lets the human triage a doc incrementally (mark a few, run apply, mark more, run apply again) without producing duplicates.

package/plugins/lisa/skills/lisa-doctor/SKILL.md

@@ -56,7 +56,10 @@ as applicable to the current repo:
    and `source` only. If a required CLI, MCP surface, or auth context is unavailable in the current
    runtime, report that explicitly instead of pretending the repo is ready.
 4. **Runtime distribution surfaces** — confirm the command, skill, hook, and related distribution
-   surfaces relevant to this repo are present where Lisa expects them on the active runtime.
+   surfaces relevant to this repo are present where Lisa expects them on the active runtime, and
+   that the Lisa-owned enforcement artifacts (`scripts/lisa-hooks/*`,
+   `scripts/lisa-enforcement-fallback.sh`) match the installed Lisa version rather than an older
+   copy. Present-but-stale is a finding: a guard whose fix never landed enforces the old behavior.
 5. **Automation readiness** — inspect whether the configured queue source/tracker and scheduling
    prerequisites are observable, but do **not** create, edit, or delete automations during doctor.
 6. **Optional GitHub Project coordination** — when `github.projects.v2` is configured, delegate

package/plugins/lisa/skills/lisa-improve-harness/SKILL.md

@@ -341,7 +341,7 @@ Any durable lesson the loop produced is **submitted** to `lisa-persist-learning`
 only write path per the `project-learnings` rule) as a candidate; its hostile-default judge — not
 this skill, and not the caller — decides the disposition. A dropped candidate is recorded in
 `Known limits`, never reported as routed or owned. This skill never writes the learnings file,
-`PROJECT_RULES.md`, or `CLAUDE.md` itself, and never promotes a learning to a higher rung (that
+host rules (`.agents/rules/`), or `CLAUDE.md` itself, and never promotes a learning to a higher rung (that
 is the gardener's ticket-gated job).
 
 ## Idempotency
@@ -483,5 +483,5 @@ its face, because a single-trajectory loop always has limits.
 - **Bounded claims.** One trajectory supports one trajectory's claim. No comparative,
   longitudinal, or population claims; `Known limits` is never empty.
 - **One write path for learnings.** Durable lessons are submitted to `lisa-persist-learning` for
-  judgment; this skill never edits the learnings ledger, `PROJECT_RULES.md`, or a rules tree,
+  judgment; this skill never edits the learnings ledger or any rules tree (host `.agents/rules/` included),
   and never promotes a learning to a higher rung.

package/plugins/lisa/skills/lisa-learnings-audit/SKILL.md

@@ -49,9 +49,12 @@ memorized list:
    — stronger than an omission count, because room was not merely tight, a real
    capture was turned away. Drain it every run (see The audit cycle).
 3. **Rules trees** — the plugin `rules/eager/` + `rules/reference/` pairs AND
-   the host project's `.claude/rules/` (e.g. `PROJECT_RULES.md`, which is
-   human-authored only — its existing sections are still audit candidates;
-   first-run candidates come from exactly there).
+   the host project's canonical host-rules directory `.agents/rules/`, plus any
+   retired-but-surviving single-file rules the project still carries
+   (`.claude/rules/PROJECT_RULES.md`, or a legacy `projectRulesFile` path).
+   All of it is human-authored only — the gardener proposes, it never rewrites —
+   and its existing sections are still audit candidates; first-run candidates
+   come from exactly there.
 4. **Skills** — `.claude/skills/` and the plugin skill roots the runtime
    exposes (descriptions are eager context; bodies load on invoke).
 5. **The wiki index** — `wiki/index.md` when the project has a wiki.

package/plugins/lisa-agy/agents/learnings-synthesizer.md

@@ -44,7 +44,7 @@ Map every finding to exactly one category. When a finding could fit two, pick th
 
 A finding that does not fit any of the eight is itself a signal — surface it under an additional ad-hoc category `Uncategorized` with a note explaining why no category fit. Better to surface than to drop.
 
-The destination column is a **hint for the human triaging the row**, not the routing decision: `lisa-debrief-apply` routes on the category, never on this column. Keep the hint honest anyway — a human decides Accept/Reject partly on where the learning will land. The three knowledge categories (recurring gotcha, process friction, convention drift) all land in the committed learnings ledger through the executable contract. Machine-local auto-memory (`project_*.md`, `MEMORY.md`), `PROJECT_RULES.md`, and `AGENTS.md` (whose `CLAUDE.md` is only a `@AGENTS.md` pointer) are **never** destinations — the first is invisible to cloud runs and teammates, and the latter two are human-authored surfaces that agents do not write.
+The destination column is a **hint for the human triaging the row**, not the routing decision: `lisa-debrief-apply` routes on the category, never on this column. Keep the hint honest anyway — a human decides Accept/Reject partly on where the learning will land. The three knowledge categories (recurring gotcha, process friction, convention drift) all land in the committed learnings ledger through the executable contract. Machine-local auto-memory (`project_*.md`, `MEMORY.md`), the host-rules directory `.agents/rules/`, and `AGENTS.md` (whose `CLAUDE.md` is only a `@AGENTS.md` pointer) are **never** destinations — the first is invisible to cloud runs and teammates, and the latter two are human-authored surfaces that agents do not write.
 
 ## Dedupe rules
 

package/plugins/lisa-agy/agents/skill-evaluator.md

@@ -18,7 +18,7 @@ Rungs are ordered by context cost and enforcement strength. Decision vocabulary:
 | Rung | Recommendation | Destination | Enters context | Admission policy |
 | --- | --- | --- | --- | --- |
 | 6 | EXECUTABLE-CONTROL | Lint / ast-grep / type / test / hook / `package.lisa.json` force | Never — diagnostic fires on violation | Mechanically decidable + stable + recurred |
-| 5 | EAGER-RULE | Auto-loaded rules tree | Unconditionally, every session | **Earned by failure evidence** (repeated misses despite retrievability); demotion-biased |
+| 5 | EAGER-RULE | Host rules: `.agents/rules/` (project scope) · plugin `rules/eager/` (upstream scope) | Unconditionally, every session | **Earned by failure evidence** (repeated misses despite retrievability); demotion-biased |
 | 4 | SKILL | `.claude/skills/<name>/SKILL.md` | Description eager; body on invoke | Procedural, complex, recognizable trigger |
 | 3 | WIKI | Wiki page + index entry | Only when routed to | Durable reference knowledge |
 | 2 | KEEP-IN-LEDGER | `PROJECT_LEARNINGS.md` (bounded contract projection) | Bounded projection only | Default landing zone; probationary, expiring |

package/plugins/lisa-agy/hooks/block-instruction-file-edits.sh

@@ -117,7 +117,7 @@ WHERE IT GOES INSTEAD — take the first one that fits:
    That is a project rule — but do not write it yourself. Capture it with
    \`/lisa:persist-learning\` so it lands in the learnings ledger with provenance
    and a confidence score. The gardener (\`/lisa:learnings:audit\`) then proposes
-   promotion into \`.claude/rules/PROJECT_RULES.md\` as a human-gated ticket.
+   promotion into the host-rules directory \`.agents/rules/\` as a human-gated ticket.
 
 2. It changes how an existing skill should behave. Edit that skill's SKILL.md.
    Knowledge belongs next to the procedure it modifies, not in a global preamble.

package/plugins/lisa-agy/hooks/block-shell-json-parsing.sh

@@ -3,7 +3,7 @@
 # Text tools (grep/sed/cut/awk) break on valid JSON — multiline values, escaped
 # quotes, reordered keys, nested objects — producing silently wrong output
 # instead of errors. jq is the required tool for structural JSON reads and
-# writes in shell. Promoted from PROJECT_RULES.md prose to an executable
+# writes in shell. Promoted from host-rules prose to an executable
 # control by the learnings gardener (issue #1787).
 #
 # Precision-first: this hook fires only on high-confidence STRUCTURAL parsing