@codyswann/lisa 4.69.1 → 4.69.2

package/README.md

@@ -288,6 +288,18 @@ into the project and unrelated Lisa stacks are not loaded. Project settings use
 `[features].hooks`; the deprecated `codex_hooks` key is removed during
 reconciliation.
 
+During an explicit Codex hook migration, including `--refresh-templates`, apply
+retains previously installed hook commands as functional regular copies with
+their helpers and rule data. An active session can keep using its loaded
+commands while a fresh session uses the current generated fallback. Host hooks
+remain intact. Keep the managed compatibility files recorded in
+`.codex/.lisa-managed.json` rather than deleting them during a running session.
+Review changed project hook definitions through Codex’s `/hooks` interface
+before trusting them in a fresh session. Automatic postinstall still skips
+agent configuration changes. This retirement
+boundary belongs to the Codex project overlay. The other supported agents do
+not delete this shell-command layout during apply.
+
 Remote coding environments use one vendor-neutral AWS bootstrap rather than
 repository-specific or agent-specific IAM users. Run `/lisa:setup-remote-aws`
 to install the common setup script and native Cursor/Copilot adapters; Claude,

package/dist/cli/doctor-legacy-overlay.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor-legacy-overlay.d.ts","sourceRoot":"","sources":["../../src/cli/doctor-legacy-overlay.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAI/C;;;;;;;;;;;GAWG;AACH,wBAAgB,uBAAuB,CAAC,UAAU,EAAE,MAAM,GAAG,WAAW,CA2CvE"}

package/dist/cli/doctor-legacy-overlay.js

@@ -1,6 +1,8 @@
-import { existsSync } from "node:fs";
+import { existsSync, lstatSync, readFileSync } from "node:fs";
 import * as path from "node:path";
 import { LISA_HOOKS_SUBDIR, LISA_RULES_SUBDIR, } from "../codex/hooks-installer.js";
+import { LISA_MANAGED_MANIFEST_FILENAME } from "../codex/manifest.js";
+import { parseHooksFile } from "../codex/hooks-merger.js";
 import { LISA_SKILLS_SUBDIR } from "../codex/skills-installer.js";
 const LEGACY_CODEX_OVERLAY_CHECK_NAME = "Codex overlay current?";
 /**
@@ -24,16 +26,20 @@ export function checkLegacyCodexOverlay(targetPath) {
             detail: "No .codex directory present",
         };
     }
+    const compatibility = hasManagedCompatibility(codexDir);
     const legacyPaths = [
         LISA_HOOKS_SUBDIR,
         LISA_RULES_SUBDIR,
         LISA_SKILLS_SUBDIR,
-    ].filter(subdir => existsSync(path.join(codexDir, subdir)));
+    ].filter(subdir => existsSync(path.join(codexDir, subdir)) &&
+        !(compatibility && subdir !== LISA_SKILLS_SUBDIR));
     if (legacyPaths.length === 0) {
         return {
             name: LEGACY_CODEX_OVERLAY_CHECK_NAME,
             status: "ok",
-            detail: "No legacy project-level Codex overlay present",
+            detail: compatibility
+                ? "Managed compatibility copies retained for active sessions; fresh sessions use the current enforcement fallback"
+                : "No legacy project-level Codex overlay present",
         };
     }
     const listed = legacyPaths
@@ -43,9 +49,35 @@ export function checkLegacyCodexOverlay(targetPath) {
         name: LEGACY_CODEX_OVERLAY_CHECK_NAME,
         status: "warn",
         detail: `Legacy pre-2.198 Codex overlay present (${listed}). ` +
-            "Run `lisa apply` in the primary checkout and commit the removals — " +
+            "Run `lisa apply` in the primary checkout to migrate the configuration and retain functional copies for active sessions — " +
             "fresh clones/worktrees otherwise load stale hooks/skills that a later " +
-            "apply deletes mid-session (CodySwannGT/lisa#1632)",
+            "apply must keep executable mid-session (CodySwannGT/lisa#1632)",
     };
 }
+/**
+ * Distinguish intentional copied compatibility from an unmigrated overlay.
+ * @param codexDir Host Codex directory.
+ * @returns Whether every recorded compatibility path remains a regular file.
+ */
+function hasManagedCompatibility(codexDir) {
+    try {
+        const manifest = JSON.parse(readFileSync(path.join(codexDir, LISA_MANAGED_MANIFEST_FILENAME), "utf8"));
+        const compatibility = manifest.hookCompatibilityFiles;
+        if (!Array.isArray(compatibility) ||
+            compatibility.length === 0 ||
+            !compatibility.every(file => typeof file === "string" &&
+                manifest.files?.includes(file) &&
+                (file.startsWith(`${LISA_HOOKS_SUBDIR}${path.sep}`) ||
+                    file.startsWith(`${LISA_RULES_SUBDIR}${path.sep}`)) &&
+                !file.split(path.sep).includes("..") &&
+                lstatSync(path.join(codexDir, file)).isFile()))
+            return false;
+        const hooks = parseHooksFile(readFileSync(path.join(codexDir, "hooks.json"), "utf8"));
+        const managed = Object.values(hooks.hooks ?? {}).flatMap(groups => groups.flatMap(group => group.hooks.filter(hook => hook._lisaManaged === true)));
+        return (managed.length === 1 && managed[0]?._lisaId === "enforcement-fallback");
+    }
+    catch {
+        return false;
+    }
+}
 //# sourceMappingURL=doctor-legacy-overlay.js.map

package/dist/cli/doctor-legacy-overlay.js.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor-legacy-overlay.js","sourceRoot":"","sources":["../../src/cli/doctor-legacy-overlay.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AAC9D,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EACL,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,6BAA6B,CAAC;AACrC,OAAO,EAAE,8BAA8B,EAAE,MAAM,sBAAsB,CAAC;AACtE,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAC1D,OAAO,EAAE,kBAAkB,EAAE,MAAM,8BAA8B,CAAC;AAGlE,MAAM,+BAA+B,GAAG,wBAAwB,CAAC;AAEjE;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,uBAAuB,CAAC,UAAkB;IACxD,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC;IACjD,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC1B,OAAO;YACL,IAAI,EAAE,+BAA+B;YACrC,MAAM,EAAE,IAAI;YACZ,MAAM,EAAE,6BAA6B;SACtC,CAAC;IACJ,CAAC;IAED,MAAM,aAAa,GAAG,uBAAuB,CAAC,QAAQ,CAAC,CAAC;IACxD,MAAM,WAAW,GAAG;QAClB,iBAAiB;QACjB,iBAAiB;QACjB,kBAAkB;KACnB,CAAC,MAAM,CACN,MAAM,CAAC,EAAE,CACP,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;QACvC,CAAC,CAAC,aAAa,IAAI,MAAM,KAAK,kBAAkB,CAAC,CACpD,CAAC;IAEF,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7B,OAAO;YACL,IAAI,EAAE,+BAA+B;YACrC,MAAM,EAAE,IAAI;YACZ,MAAM,EAAE,aAAa;gBACnB,CAAC,CAAC,gHAAgH;gBAClH,CAAC,CAAC,+CAA+C;SACpD,CAAC;IACJ,CAAC;IAED,MAAM,MAAM,GAAG,WAAW;SACvB,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;SAC1C,IAAI,CAAC,IAAI,CAAC,CAAC;IACd,OAAO;QACL,IAAI,EAAE,+BAA+B;QACrC,MAAM,EAAE,MAAM;QACd,MAAM,EACJ,2CAA2C,MAAM,KAAK;YACtD,2HAA2H;YAC3H,wEAAwE;YACxE,gEAAgE;KACnE,CAAC;AACJ,CAAC;AAED;;;;GAIG;AACH,SAAS,uBAAuB,CAAC,QAAgB;IAC/C,IAAI,CAAC;QACH,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CACzB,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,8BAA8B,CAAC,EAAE,MAAM,CAAC,CACf,CAAC;QAC7D,MAAM,aAAa,GAAG,QAAQ,CAAC,sBAAsB,CAAC;QACtD,IACE,CAAC,KAAK,CAAC,OAAO,CAAC,aAAa,CAAC;YAC7B,aAAa,CAAC,MAAM,KAAK,CAAC;YAC1B,CAAC,aAAa,CAAC,KAAK,CAClB,IAAI,CAAC,EAAE,CACL,OAAO,IAAI,KAAK,QAAQ;gBACxB,QAAQ,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,CAAC;gBAC9B,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,iBAAiB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;oBACjD,IAAI,CAAC,UAAU,CAAC,GAAG,iBAAiB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC;gBACrD,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC;gBACpC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,MAAM,EAAE,CAChD;YAED,OAAO,KAAK,CAAC;QACf,MAAM,KAAK,GAAG,cAAc,CAC1B,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,CAAC,CACxD,CAAC;QACF,MAAM,OAAO,GAAG,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAChE,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CACrB,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,KAAK,IAAI,CAAC,CACvD,CACF,CAAC;QACF,OAAO,CACL,OAAO,CAAC,MAAM,KAAK,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,OAAO,KAAK,sBAAsB,CACvE,CAAC;IACJ,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,KAAK,CAAC;IACf,CAAC;AACH,CAAC"}

package/dist/codex/hooks-installer.d.ts

@@ -55,4 +55,16 @@ export interface HooksInstallResult {
  * @returns Result describing what was written
  */
 export declare function installHooks(lisaDir: string, destDir: string, detectedTypes: readonly ProjectType[], previousManagedFiles?: readonly string[]): Promise<HooksInstallResult>;
+/**
+ * Keep previously installed catalog commands functional without registering
+ * them again. Copies outlive replacement of the package that owned old links.
+ * Host-authored siblings are never pruned. This is an apply-time migration,
+ * not runtime/session detection or an assumed hot-reload boundary.
+ * @param lisaDir Lisa source/package root.
+ * @param destDir Host root.
+ * @param detectedTypes Current project types.
+ * @param previousManagedFiles Previous manifest ownership.
+ * @returns Compatibility files to retain in the current manifest.
+ */
+export declare function installHookCompatibility(lisaDir: string, destDir: string, detectedTypes: readonly ProjectType[], previousManagedFiles: readonly string[]): Promise<readonly string[]>;
 //# sourceMappingURL=hooks-installer.d.ts.map

package/dist/codex/hooks-installer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"hooks-installer.d.ts","sourceRoot":"","sources":["../../src/codex/hooks-installer.ts"],"names":[],"mappings":"AAkCA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAWrD,kEAAkE;AAClE,eAAO,MAAM,iBAAiB,QAA6B,CAAC;AAE5D;;;;;GAKG;AACH,eAAO,MAAM,cAAc,2BAA2B,CAAC;AAEvD;;;;;;;GAOG;AACH,eAAO,MAAM,aAAa,sBAAsB,CAAC;AAEjD,kFAAkF;AAClF,eAAO,MAAM,iBAAiB,eAAe,CAAC;AAE9C,+DAA+D;AAC/D,eAAO,MAAM,cAAc,eAAe,CAAC;AAmL3C;;;;;;;;;;;;;GAaG;AACH,eAAO,MAAM,sBAAsB,EAAE,SAAS,MAAM,EAInD,CAAC;AAEF,uCAAuC;AACvC,MAAM,WAAW,kBAAkB;IACjC,yEAAyE;IACzE,QAAQ,CAAC,YAAY,EAAE,SAAS,MAAM,EAAE,CAAC;IACzC,0DAA0D;IAC1D,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,iEAAiE;IACjE,QAAQ,CAAC,OAAO,EAAE,SAAS,MAAM,EAAE,CAAC;CACrC;AAED;;;;;;;;GAQG;AACH,wBAAsB,YAAY,CAChC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,SAAS,WAAW,EAAE,EACrC,oBAAoB,GAAE,SAAS,MAAM,EAAO,GAC3C,OAAO,CAAC,kBAAkB,CAAC,CAsF7B"}
+{"version":3,"file":"hooks-installer.d.ts","sourceRoot":"","sources":["../../src/codex/hooks-installer.ts"],"names":[],"mappings":"AA2CA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAWrD,kEAAkE;AAClE,eAAO,MAAM,iBAAiB,QAA6B,CAAC;AAE5D;;;;;GAKG;AACH,eAAO,MAAM,cAAc,2BAA2B,CAAC;AAEvD;;;;;;;GAOG;AACH,eAAO,MAAM,aAAa,sBAAsB,CAAC;AAEjD,kFAAkF;AAClF,eAAO,MAAM,iBAAiB,eAAe,CAAC;AAE9C,+DAA+D;AAC/D,eAAO,MAAM,cAAc,eAAe,CAAC;AAqL3C;;;;;;;;;;;;;GAaG;AACH,eAAO,MAAM,sBAAsB,EAAE,SAAS,MAAM,EAInD,CAAC;AAEF,uCAAuC;AACvC,MAAM,WAAW,kBAAkB;IACjC,yEAAyE;IACzE,QAAQ,CAAC,YAAY,EAAE,SAAS,MAAM,EAAE,CAAC;IACzC,0DAA0D;IAC1D,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,iEAAiE;IACjE,QAAQ,CAAC,OAAO,EAAE,SAAS,MAAM,EAAE,CAAC;CACrC;AAED;;;;;;;;GAQG;AACH,wBAAsB,YAAY,CAChC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,SAAS,WAAW,EAAE,EACrC,oBAAoB,GAAE,SAAS,MAAM,EAAO,GAC3C,OAAO,CAAC,kBAAkB,CAAC,CAsF7B;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,wBAAwB,CAC5C,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,SAAS,WAAW,EAAE,EACrC,oBAAoB,EAAE,SAAS,MAAM,EAAE,GACtC,OAAO,CAAC,SAAS,MAAM,EAAE,CAAC,CAmE5B"}

package/dist/codex/hooks-installer.js

@@ -25,11 +25,11 @@
  * The project overlay now uses plugin-bundled hooks for the complete catalog
  * and one repository-owned enforcement dispatcher as the fail-closed delivery
  * fallback. This module remains for migration coverage of the retired linked
- * script/rule layout.
+ * script/rule layout and source-owned compatibility copies for loaded sessions.
  * @module codex/hooks-installer
  */
 import * as fse from "fs-extra";
-import { readFile, rm, symlink, writeFile } from "node:fs/promises";
+import { lstat, mkdtemp, readFile, readlink, rename, rm, symlink, writeFile, } from "node:fs/promises";
 import * as path from "node:path";
 import { fileURLToPath } from "node:url";
 import { mirrorLisaRules } from "../core/lisa-rules-mirror.js";
@@ -62,6 +62,7 @@ export const HOOKS_FILENAME = "hooks.json";
  * its three write paths (text Edit, file Write, apply_patch diff).
  */
 const WRITE_MATCHER = "Edit|Write|apply_patch";
+const INJECT_RULES_ID = "inject-rules";
 const HARPER_PLUGIN = "lisa-harper-fabric";
 /**
  * Hook catalog. Adding a new hook? Three steps:
@@ -74,7 +75,7 @@ const HARPER_PLUGIN = "lisa-harper-fabric";
  */
 const HOOK_CATALOG = [
     {
-        id: "inject-rules",
+        id: INJECT_RULES_ID,
         event: "SessionStart",
         matcher: "",
         scriptFilename: "inject-rules.sh",
@@ -110,6 +111,7 @@ const HOOK_CATALOG = [
         event: "PreToolUse",
         matcher: "Bash",
         scriptFilename: "block-direct-issue-create.sh",
+        sourcePlugin: "lisa",
         forProjectTypes: ["*"],
         statusMessage: "Checking work-item filing policy",
     },
@@ -256,7 +258,7 @@ export async function installHooks(lisaDir, destDir, detectedTypes, previousMana
         : [];
     // Step 2: mirror rules from Lisa into .codex/lisa-rules/ (only when
     // inject-rules is being installed — i.e., always, since it's a "*" hook)
-    const ruleFiles = applicable.some(e => e.id === "inject-rules")
+    const ruleFiles = applicable.some(e => e.id === INJECT_RULES_ID)
         ? (await mirrorLisaRules(lisaDir, rulesDir, detectedTypes, "link")).map(file => path.join(LISA_RULES_SUBDIR, file))
         : [];
     // Step 3: tagged-merge hooks.json
@@ -279,6 +281,245 @@ export async function installHooks(lisaDir, destDir, detectedTypes, previousMana
         deleted: Object.freeze(deleted),
     };
 }
+/**
+ * Keep previously installed catalog commands functional without registering
+ * them again. Copies outlive replacement of the package that owned old links.
+ * Host-authored siblings are never pruned. This is an apply-time migration,
+ * not runtime/session detection or an assumed hot-reload boundary.
+ * @param lisaDir Lisa source/package root.
+ * @param destDir Host root.
+ * @param detectedTypes Current project types.
+ * @param previousManagedFiles Previous manifest ownership.
+ * @returns Compatibility files to retain in the current manifest.
+ */
+export async function installHookCompatibility(lisaDir, destDir, detectedTypes, previousManagedFiles) {
+    const codexDir = path.join(destDir, ".codex");
+    const hooksDir = path.join(codexDir, LISA_HOOKS_SUBDIR);
+    const existing = await readHooksFile(path.join(codexDir, HOOKS_FILENAME));
+    const taggedCommands = new Set(Object.values(existing.hooks ?? {}).flatMap(groups => groups.flatMap(group => group.hooks
+        .filter(hook => hook._lisaManaged === true)
+        .map(hook => hook.command))));
+    const owned = new Set([
+        ...previousManagedFiles,
+        ...HOOK_CATALOG.filter(entry => taggedCommands.has(catalogEntryToSpec(entry, destDir).command)).map(entry => path.join(LISA_HOOKS_SUBDIR, entry.scriptFilename)),
+    ]);
+    const candidates = await Promise.all(HOOK_CATALOG.map(async (entry) => {
+        const relative = path.join(LISA_HOOKS_SUBDIR, entry.scriptFilename);
+        const keep = owned.has(relative) ||
+            taggedCommands.has(catalogEntryToSpec(entry, destDir).command) ||
+            (await isManagedSourceLink(path.join(codexDir, relative), resolveHookScript(lisaDir, entry), lisaDir, destDir));
+        return keep ? entry : undefined;
+    }));
+    const retained = candidates.filter((entry) => entry !== undefined);
+    if (retained.length === 0)
+        return [];
+    const sources = compatibilitySources(lisaDir, retained);
+    await assertCompatibilityOwnership(sources, codexDir, owned, lisaDir, destDir);
+    await fse.ensureDir(hooksDir);
+    const entrypoints = new Set(retained.map(entry => entry.scriptFilename));
+    const rules = retained.some(entry => entry.id === INJECT_RULES_ID)
+        ? await copyCompatibilityRules(lisaDir, codexDir, detectedTypes, retained, owned)
+        : [];
+    // Install complete dependencies before atomically replacing loaded entrypoints.
+    const helpers = await copyCompatibilitySources(sources.filter(source => !entrypoints.has(source.filename)), codexDir);
+    const scripts = await copyCompatibilitySources(sources.filter(source => entrypoints.has(source.filename)), codexDir);
+    return Object.freeze([...scripts, ...helpers, ...rules]);
+}
+/**
+ * Reject unknown companion collisions before changing any compatibility file.
+ * A retained command does not grant ownership of a host-authored helper.
+ * @param sources Complete catalog closure.
+ * @param codexDir Host Codex root.
+ * @param owned Proven manifest/tagged-handler ownership.
+ * @param lisaDir Verified Lisa package root.
+ * @param destDir Host root.
+ */
+async function assertCompatibilityOwnership(sources, codexDir, owned, lisaDir, destDir) {
+    await Promise.all(sources.map(async ({ source, filename }) => {
+        const relative = path.join(LISA_HOOKS_SUBDIR, filename);
+        const destination = path.join(codexDir, relative);
+        const stat = await lstat(destination).catch(error => {
+            if (error.code === "ENOENT")
+                return undefined;
+            throw error;
+        });
+        if (!stat || owned.has(relative))
+            return;
+        if (stat.isSymbolicLink()) {
+            if (await isManagedSourceLink(destination, source, lisaDir, destDir))
+                return;
+        }
+        else if (stat.isFile() &&
+            (await readFile(destination)).equals(await readFile(source))) {
+            return;
+        }
+        throw new Error(`Cannot migrate Codex hooks: .codex/${relative} contains host-owned content. No compatibility files were changed. Preserve it and resolve the source ownership conflict before applying again.`);
+    }));
+}
+/**
+ * Copy one dependency group before exposing dependent entrypoints.
+ * @param sources Package implementations.
+ * @param codexDir Host Codex directory.
+ * @returns Installed paths.
+ */
+async function copyCompatibilitySources(sources, codexDir) {
+    return Promise.all(sources.map(async ({ source, filename }) => {
+        const relative = path.join(LISA_HOOKS_SUBDIR, filename);
+        await copyManagedCompatibility(source, path.join(codexDir, relative));
+        return relative;
+    }));
+}
+/**
+ * Resolve the full helper/data closure from the existing hook catalog.
+ * @param lisaDir Source/package root.
+ * @param retained Previously installed catalog entries.
+ * @returns Script and companion sources.
+ */
+function compatibilitySources(lisaDir, retained) {
+    const helpers = [
+        ...(retained.some(entry => entry.needsEditPathLib) ? [EDIT_PATHS_LIB] : []),
+        ...(retained.some(entry => entry.needsEditGate) ? [EDIT_GATE_LIB] : []),
+    ];
+    return [
+        ...retained.map(entry => ({
+            source: resolveHookScript(lisaDir, entry),
+            filename: entry.scriptFilename,
+        })),
+        ...helpers.map(filename => ({
+            source: resolveBundledScript(filename),
+            filename,
+        })),
+        ...(retained.some(entry => entry.sourcePlugin === "lisa")
+            ? [
+                {
+                    source: path.join(lisaDir, "plugins/lisa/hooks/guard-dedupe.bash"),
+                    filename: "guard-dedupe.bash",
+                },
+            ]
+            : []),
+        ...(retained.some(entry => entry.sourcePlugin === HARPER_PLUGIN)
+            ? harperSupportSources(lisaDir)
+            : []),
+    ];
+}
+/**
+ * Copy rule dependencies without replacing host-authored rules.
+ * @param lisaDir Source/package root.
+ * @param codexDir Host Codex directory.
+ * @param detectedTypes Current types.
+ * @param retained Entries determining required earlier stack rules.
+ * @param owned Prior manifest paths.
+ * @returns Copied rule paths.
+ */
+async function copyCompatibilityRules(lisaDir, codexDir, detectedTypes, retained, owned) {
+    const ruleTypes = [
+        ...new Set([
+            ...detectedTypes,
+            ...retained.flatMap(entry => entry.forProjectTypes.filter(type => type !== "*")),
+        ]),
+    ];
+    const scratch = await mkdtemp(path.join(codexDir, ".compat-rules-"));
+    try {
+        const rules = await mirrorLisaRules(lisaDir, scratch, ruleTypes, "link");
+        const copied = await Promise.all(rules.map(async (relativeRule) => {
+            const relative = path.join(LISA_RULES_SUBDIR, relativeRule);
+            const destination = path.join(codexDir, relative);
+            const stat = await lstat(destination).catch(() => undefined);
+            const source = await readlink(path.join(scratch, relativeRule));
+            const linkedRule = stat?.isSymbolicLink() &&
+                (await isManagedSourceLink(destination, source, lisaDir, path.dirname(codexDir)));
+            if (stat && !linkedRule && !owned.has(relative))
+                return undefined;
+            await fse.ensureDir(path.dirname(destination));
+            await copyManagedCompatibility(path.join(scratch, relativeRule), destination);
+            return relative;
+        }));
+        return copied.filter((file) => file !== undefined);
+    }
+    finally {
+        await rm(scratch, { recursive: true, force: true });
+    }
+}
+/**
+ * Admit links to known Lisa sources, not host paths with similar suffixes.
+ * Canonical installed-package paths also recover genuinely dangling links.
+ * @param destination Host script path.
+ * @param source Exact shipped source.
+ * @param lisaDir Verified Lisa package root.
+ * @param destDir Host root.
+ * @returns Whether the catalog owns this legacy representation.
+ */
+async function isManagedSourceLink(destination, source, lisaDir, destDir) {
+    const stat = await lstat(destination).catch(() => undefined);
+    if (!stat?.isSymbolicLink())
+        return false;
+    const target = path.resolve(path.dirname(destination), await readlink(destination));
+    const relative = path.relative(lisaDir, source);
+    if (target === path.resolve(source))
+        return true;
+    if (relative.startsWith(`..${path.sep}`) || path.isAbsolute(relative))
+        return false;
+    const variants = sourceLocationVariants(relative);
+    if (variants.some(file => target === path.resolve(lisaDir, file)))
+        return true;
+    const installedRoot = path.join(destDir, "node_modules/@codyswann/lisa");
+    return isLisaPackageTarget(target, variants, installedRoot);
+}
+/**
+ * Source and compiled trees contain the same legacy bundled scripts.
+ * @param relative Source path within the verified Lisa package.
+ * @returns Exact supported source locations within that package.
+ */
+function sourceLocationVariants(relative) {
+    const tree = ["src", "dist"].find(directory => relative.startsWith(path.join(directory, "codex", "scripts") + path.sep));
+    return tree === undefined
+        ? [relative]
+        : [
+            relative,
+            path.join(tree === "src" ? "dist" : "src", "codex", "scripts", path.basename(relative)),
+        ];
+}
+/**
+ * Verify old package/store roots rather than relying on their directory layout.
+ * @param target Resolved legacy link target.
+ * @param variants Exact supported paths within a Lisa package.
+ * @param installedRoot Canonical host package path, including dangling installs.
+ * @returns Whether positive package identity owns this expected source path.
+ */
+async function isLisaPackageTarget(target, variants, installedRoot) {
+    const roots = variants
+        .filter(file => target.endsWith(path.sep + file))
+        .map(file => target.slice(0, -(file.length + 1)));
+    const verified = await Promise.all(roots.map(async (root) => {
+        if (root === path.resolve(installedRoot) && !(await fse.pathExists(root)))
+            return true;
+        const metadata = await readFile(path.join(root, "package.json"), "utf8")
+            .then(raw => JSON.parse(raw))
+            .catch(() => undefined);
+        return (typeof metadata === "object" &&
+            metadata !== null &&
+            "name" in metadata &&
+            metadata.name === "@codyswann/lisa");
+    }));
+    return verified.some(Boolean);
+}
+/**
+ * Replace a managed representation with executable regular source bytes.
+ * @param source Functional shipped implementation.
+ * @param destination Old loaded-command path.
+ */
+async function copyManagedCompatibility(source, destination) {
+    const content = await readFile(source);
+    const scratch = await mkdtemp(path.join(path.dirname(destination), ".compat-file-"));
+    try {
+        const replacement = path.join(scratch, "replacement");
+        await writeFile(replacement, content, { mode: 0o755 });
+        await rename(replacement, destination);
+    }
+    finally {
+        await rm(scratch, { force: true, recursive: true });
+    }
+}
 /** Project-local directory prefixes wholly owned by the hook installer. */
 const MANAGED_HOOK_PREFIXES = [
     `${LISA_HOOKS_SUBDIR}${path.sep}`,
@@ -374,7 +615,17 @@ function resolveHookScript(lisaDir, entry) {
  * @returns Managed paths relative to `.codex/`.
  */
 async function linkHarperSupportFiles(lisaDir, hooksDir) {
-    const sources = [
+    const sources = harperSupportSources(lisaDir);
+    await Promise.all(sources.map(({ source, filename }) => linkManagedFile(source, path.join(hooksDir, filename))));
+    return sources.map(({ filename }) => path.join(LISA_HOOKS_SUBDIR, filename));
+}
+/**
+ * Companion sources shared by linked installation and copied compatibility.
+ * @param lisaDir Lisa package root.
+ * @returns Complete Harper companion list.
+ */
+function harperSupportSources(lisaDir) {
+    return [
         {
             source: path.join(lisaDir, "plugins", HARPER_PLUGIN, "hooks", "enforce-config-extensions.mjs"),
             filename: "enforce-config-extensions.mjs",
@@ -384,8 +635,6 @@ async function linkHarperSupportFiles(lisaDir, hooksDir) {
             filename: "generated-artifact-globs.txt",
         },
     ];
-    await Promise.all(sources.map(({ source, filename }) => linkManagedFile(source, path.join(hooksDir, filename))));
-    return sources.map(({ filename }) => path.join(LISA_HOOKS_SUBDIR, filename));
 }
 /**
  * Replace a Lisa-owned project file with a link to its package source.

package/dist/codex/hooks-installer.js.map

@@ -1 +1 @@
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package/dist/codex/manifest.d.ts

@@ -7,6 +7,8 @@ export interface LisaManagedManifest {
      * Used to identify which files to delete when they stop being shipped.
      */
     readonly files: readonly string[];
+    /** Intentional copied commands/data retained for already-loaded sessions. */
+    readonly hookCompatibilityFiles?: readonly string[];
 }
 /**
  * Read the Lisa-managed manifest from `<destDir>/.codex/.lisa-managed.json`.
@@ -19,8 +21,9 @@ export declare function readManagedManifest(destDir: string): Promise<LisaManage
  * Write the Lisa-managed manifest to disk, replacing any existing content.
  * @param destDir - Absolute path to the destination project root
  * @param files - Sorted list of relative-to-`.codex/` file paths Lisa shipped
+ * @param hookCompatibilityFiles Intentional copied legacy paths.
  */
-export declare function writeManagedManifest(destDir: string, files: readonly string[]): Promise<void>;
+export declare function writeManagedManifest(destDir: string, files: readonly string[], hookCompatibilityFiles?: readonly string[]): Promise<void>;
 /**
  * Compute the set of stale files: in the previous manifest but not in the
  * new shipment. These are candidates for deletion.

package/dist/codex/manifest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/codex/manifest.ts"],"names":[],"mappings":"AAuBA,mEAAmE;AACnE,eAAO,MAAM,8BAA8B,uBAAuB,CAAC;AAEnE,4CAA4C;AAC5C,MAAM,WAAW,mBAAmB;IAClC;;;OAGG;IACH,QAAQ,CAAC,KAAK,EAAE,SAAS,MAAM,EAAE,CAAC;CACnC;AAED;;;;;GAKG;AACH,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,mBAAmB,CAAC,CAY9B;AAED;;;;GAIG;AACH,wBAAsB,oBAAoB,CACxC,OAAO,EAAE,MAAM,EACf,KAAK,EAAE,SAAS,MAAM,EAAE,GACvB,OAAO,CAAC,IAAI,CAAC,CAYf;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,mBAAmB,EAC7B,OAAO,EAAE,SAAS,MAAM,EAAE,GACzB,SAAS,MAAM,EAAE,CAGnB"}
+{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/codex/manifest.ts"],"names":[],"mappings":"AAuBA,mEAAmE;AACnE,eAAO,MAAM,8BAA8B,uBAAuB,CAAC;AAEnE,4CAA4C;AAC5C,MAAM,WAAW,mBAAmB;IAClC;;;OAGG;IACH,QAAQ,CAAC,KAAK,EAAE,SAAS,MAAM,EAAE,CAAC;IAClC,6EAA6E;IAC7E,QAAQ,CAAC,sBAAsB,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;CACrD;AAED;;;;;GAKG;AACH,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,mBAAmB,CAAC,CAY9B;AAED;;;;;GAKG;AACH,wBAAsB,oBAAoB,CACxC,OAAO,EAAE,MAAM,EACf,KAAK,EAAE,SAAS,MAAM,EAAE,EACxB,sBAAsB,GAAE,SAAS,MAAM,EAAO,GAC7C,OAAO,CAAC,IAAI,CAAC,CAef;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,mBAAmB,EAC7B,OAAO,EAAE,SAAS,MAAM,EAAE,GACzB,SAAS,MAAM,EAAE,CAGnB"}

package/dist/codex/manifest.js

@@ -41,13 +41,17 @@ export async function readManagedManifest(destDir) {
  * Write the Lisa-managed manifest to disk, replacing any existing content.
  * @param destDir - Absolute path to the destination project root
  * @param files - Sorted list of relative-to-`.codex/` file paths Lisa shipped
+ * @param hookCompatibilityFiles Intentional copied legacy paths.
  */
-export async function writeManagedManifest(destDir, files) {
+export async function writeManagedManifest(destDir, files, hookCompatibilityFiles = []) {
     const codexDir = path.join(destDir, ".codex");
     await fse.ensureDir(codexDir);
     const manifestPath = path.join(codexDir, LISA_MANAGED_MANIFEST_FILENAME);
     const manifest = {
         files: [...files].sort((a, b) => a.localeCompare(b)),
+        ...(hookCompatibilityFiles.length > 0
+            ? { hookCompatibilityFiles: [...hookCompatibilityFiles] }
+            : {}),
     };
     await writeFile(manifestPath, `${JSON.stringify(manifest, null, 2)}\n`, "utf8");
 }
@@ -81,6 +85,18 @@ function validateManifest(parsed, manifestPath) {
     if (files.length !== obj.files.length) {
         throw new Error(`Invalid Lisa-managed manifest at ${manifestPath}: "files" must contain only strings`);
     }
-    return { files: Object.freeze(files) };
+    if (obj.hookCompatibilityFiles !== undefined &&
+        (!Array.isArray(obj.hookCompatibilityFiles) ||
+            obj.hookCompatibilityFiles.some(file => typeof file !== "string" || !files.includes(file)))) {
+        throw new Error(`Invalid Lisa-managed manifest at ${manifestPath}: compatibility files must be managed files`);
+    }
+    return {
+        files: Object.freeze(files),
+        ...(obj.hookCompatibilityFiles !== undefined
+            ? {
+                hookCompatibilityFiles: Object.freeze(obj.hookCompatibilityFiles),
+            }
+            : {}),
+    };
 }
 //# sourceMappingURL=manifest.js.map

package/dist/codex/manifest.js.map

@@ -1 +1 @@
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package/dist/codex/project-hooks-cleanup.d.ts

@@ -3,10 +3,10 @@ export interface ProjectHooksCleanupResult {
     readonly deleted: readonly string[];
 }
 /**
- * Remove only Lisa-tagged hook handlers and Lisa-owned legacy directories.
+ * Remove only Lisa-tagged handlers. Loaded commands still need their files.
  * @param destDir Host project root.
- * @param previousManagedFiles Previous `.codex` ownership entries.
+ * @param _previousManagedFiles Previous `.codex` ownership entries.
  * @returns Removed Lisa-owned paths.
  */
-export declare function retireProjectHooks(destDir: string, previousManagedFiles: readonly string[]): Promise<ProjectHooksCleanupResult>;
+export declare function retireProjectHooks(destDir: string, _previousManagedFiles: readonly string[]): Promise<ProjectHooksCleanupResult>;
 //# sourceMappingURL=project-hooks-cleanup.d.ts.map

package/dist/codex/project-hooks-cleanup.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"project-hooks-cleanup.d.ts","sourceRoot":"","sources":["../../src/codex/project-hooks-cleanup.ts"],"names":[],"mappings":"AAWA,6CAA6C;AAC7C,MAAM,WAAW,yBAAyB;IACxC,QAAQ,CAAC,OAAO,EAAE,SAAS,MAAM,EAAE,CAAC;CACrC;AAED;;;;;GAKG;AACH,wBAAsB,kBAAkB,CACtC,OAAO,EAAE,MAAM,EACf,qBAAqB,EAAE,SAAS,MAAM,EAAE,GACvC,OAAO,CAAC,yBAAyB,CAAC,CAQpC"}