@indigoai-us/hq-cloud 6.1.0 → 6.2.0

package/dist/index.js

@@ -42,9 +42,9 @@ export { invite, listInvites, revokeInvite } from "./cli/index.js";
 export { accept, parseToken } from "./cli/index.js";
 export { promote } from "./cli/index.js";
 // Skill/personal-overlay mirroring + workers-registry regen (`hq reindex`).
-export { reindex, reindexScriptPath } from "./cli/index.js";
+export { reindex } from "./cli/index.js";
 // Drift-preserving HQ-core re-sync — shared by the HQ Sync app and `hq rescue`.
-export { rescue, rescueScriptPath, buildRescueArgs } from "./cli/index.js";
+export { rescue, buildRescueArgs } from "./cli/index.js";
 // Client identification — every first-party caller should construct one of
 // these once at startup and pass it in via VaultServiceConfig.clientInfo.
 export { buildClientHeaders, clientInfoFromPackage, detectHqCoreVersion, HEADER_CLIENT_NAME, HEADER_CLIENT_VERSION, HEADER_HQ_CORE_VERSION, } from "./client-info.js";

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/lib/conflict-index.d.ts

@@ -63,4 +63,44 @@ export declare function appendConflictEntry(hqRoot: string, entry: ConflictIndex
  * skill — we want that to be a clean exit, not an error).
  */
 export declare function removeConflictEntry(hqRoot: string, id: string): void;
+/** Summary of what a {@link pruneConflictIndex} pass reclaimed. */
+export interface PruneConflictIndexResult {
+    /** Rows dropped because their `.conflict-*` mirror no longer exists. */
+    prunedOrphans: number;
+    /** Rows dropped because the original file and its mirror are byte-identical. */
+    prunedIdentical: number;
+    /** Byte-identical mirror files deleted from disk during the pass. */
+    removedMirrors: number;
+    /** Rows kept (genuine divergence, or unprovable — fail-safe retained). */
+    kept: number;
+}
+/**
+ * Garbage-collect the conflict index so it self-heals instead of growing
+ * without bound. Before this pass existed the ledger only ever shrank when a
+ * human resolved a conflict via `/resolve-conflicts`; every false positive and
+ * every orphaned row lingered forever, so the index over-reported the real
+ * pending-conflict count (the menubar's journal-derived count stayed correct,
+ * but `.hq-conflicts/index.json` did not).
+ *
+ * Two classes of entry are dropped — both provably not a pending conflict:
+ *
+ *   1. **Orphaned** — the `.conflict-*` mirror file is gone from disk. The
+ *      mirror is the only artifact a human resolves against; once it's missing
+ *      the row can never be acted on, so it's pure litter (the "missing-cloud"
+ *      rows operators reported climbing into the dozens).
+ *
+ *   2. **Byte-identical false positives** — the original file and its conflict
+ *      mirror both still exist and are byte-for-byte identical. The mirror
+ *      holds the remote bytes captured at detection time, so identical bytes
+ *      mean there was never a real divergence (this is exactly the manual
+ *      safe-purge operators have been doing by hand). The stale mirror file is
+ *      deleted and the row dropped.
+ *
+ * Conservative by construction — an entry is kept whenever it might be a real
+ * conflict: the original file is missing (a genuine local-delete-vs-remote
+ * divergence), the bytes differ, or either side can't be read. The index file
+ * is only rewritten when at least one row is actually dropped, so a clean
+ * ledger keeps its mtime untouched.
+ */
+export declare function pruneConflictIndex(hqRoot: string): PruneConflictIndexResult;
 //# sourceMappingURL=conflict-index.d.ts.map

package/dist/lib/conflict-index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"conflict-index.d.ts","sourceRoot":"","sources":["../../src/lib/conflict-index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;GAmBG;AAKH,OAAO,KAAK,EAAE,aAAa,EAAE,kBAAkB,EAAE,MAAM,aAAa,CAAC;AAKrE;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED;;;;;;;;GAQG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,MAAM,GAAG,aAAa,CAY/D;AAED;;;;;;;;GAQG;AACH,wBAAgB,kBAAkB,CAChC,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,aAAa,GACnB,IAAI,CAgBN;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,kBAAkB,GACxB,IAAI,CASN;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,GAAG,IAAI,CAKpE;AAED,mEAAmE;AACnE,MAAM,WAAW,wBAAwB;IACvC,wEAAwE;IACxE,aAAa,EAAE,MAAM,CAAC;IACtB,gFAAgF;IAChF,eAAe,EAAE,MAAM,CAAC;IACxB,qEAAqE;IACrE,cAAc,EAAE,MAAM,CAAC;IACvB,0EAA0E;IAC1E,IAAI,EAAE,MAAM,CAAC;CACd;AA4BD;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,MAAM,GAAG,wBAAwB,CA8E3E"}

package/dist/lib/conflict-index.js

@@ -109,4 +109,125 @@ export function removeConflictEntry(hqRoot, id) {
         return;
     writeConflictIndex(hqRoot, { version: index.version, conflicts: filtered });
 }
+/**
+ * Byte-identity check used by the prune pass. Symlink-aware: two symlinks are
+ * identical iff their link targets match (mirroring how the detector hashes a
+ * symlink record — `hashSymlinkTarget`, not the followed content). A symlink
+ * compared against a regular file is never identical. Regular files reject on a
+ * size mismatch first (cheap), then compare full bytes.
+ *
+ * Throws if either side can't be read — callers treat that as "unprovable" and
+ * keep the entry rather than risk dropping a real conflict.
+ */
+function entryFilesAreIdentical(aPath, aStat, bPath, bStat) {
+    const aLink = aStat.isSymbolicLink();
+    const bLink = bStat.isSymbolicLink();
+    if (aLink || bLink) {
+        if (aLink !== bLink)
+            return false;
+        return fs.readlinkSync(aPath) === fs.readlinkSync(bPath);
+    }
+    if (aStat.size !== bStat.size)
+        return false;
+    return fs.readFileSync(aPath).equals(fs.readFileSync(bPath));
+}
+/**
+ * Garbage-collect the conflict index so it self-heals instead of growing
+ * without bound. Before this pass existed the ledger only ever shrank when a
+ * human resolved a conflict via `/resolve-conflicts`; every false positive and
+ * every orphaned row lingered forever, so the index over-reported the real
+ * pending-conflict count (the menubar's journal-derived count stayed correct,
+ * but `.hq-conflicts/index.json` did not).
+ *
+ * Two classes of entry are dropped — both provably not a pending conflict:
+ *
+ *   1. **Orphaned** — the `.conflict-*` mirror file is gone from disk. The
+ *      mirror is the only artifact a human resolves against; once it's missing
+ *      the row can never be acted on, so it's pure litter (the "missing-cloud"
+ *      rows operators reported climbing into the dozens).
+ *
+ *   2. **Byte-identical false positives** — the original file and its conflict
+ *      mirror both still exist and are byte-for-byte identical. The mirror
+ *      holds the remote bytes captured at detection time, so identical bytes
+ *      mean there was never a real divergence (this is exactly the manual
+ *      safe-purge operators have been doing by hand). The stale mirror file is
+ *      deleted and the row dropped.
+ *
+ * Conservative by construction — an entry is kept whenever it might be a real
+ * conflict: the original file is missing (a genuine local-delete-vs-remote
+ * divergence), the bytes differ, or either side can't be read. The index file
+ * is only rewritten when at least one row is actually dropped, so a clean
+ * ledger keeps its mtime untouched.
+ */
+export function pruneConflictIndex(hqRoot) {
+    const result = {
+        prunedOrphans: 0,
+        prunedIdentical: 0,
+        removedMirrors: 0,
+        kept: 0,
+    };
+    const index = readConflictIndex(hqRoot);
+    if (index.conflicts.length === 0)
+        return result;
+    const kept = [];
+    const mirrorsToRemove = [];
+    for (const entry of index.conflicts) {
+        const mirrorAbs = path.join(hqRoot, entry.conflictPath);
+        const originalAbs = path.join(hqRoot, entry.originalPath);
+        let mirrorStat;
+        try {
+            mirrorStat = fs.lstatSync(mirrorAbs);
+        }
+        catch {
+            // Mirror is gone — orphaned row, drop it. Nothing on disk to clean up.
+            result.prunedOrphans++;
+            continue;
+        }
+        // Both sides must exist to compare. A missing original is a real
+        // local-delete divergence — keep it for the human to resolve.
+        let originalStat;
+        try {
+            originalStat = fs.lstatSync(originalAbs);
+        }
+        catch {
+            kept.push(entry);
+            result.kept++;
+            continue;
+        }
+        let identical;
+        try {
+            identical = entryFilesAreIdentical(originalAbs, originalStat, mirrorAbs, mirrorStat);
+        }
+        catch {
+            // Couldn't read one side — fail safe, keep the row.
+            kept.push(entry);
+            result.kept++;
+            continue;
+        }
+        if (identical) {
+            result.prunedIdentical++;
+            mirrorsToRemove.push(mirrorAbs);
+        }
+        else {
+            kept.push(entry);
+            result.kept++;
+        }
+    }
+    // No row dropped → leave the file (and its mtime) untouched.
+    if (kept.length === index.conflicts.length)
+        return result;
+    // Delete the byte-identical mirror litter. Best-effort: a leftover identical
+    // mirror is cosmetic, never corrupting, so a failed unlink doesn't abort.
+    for (const mirrorAbs of mirrorsToRemove) {
+        try {
+            fs.rmSync(mirrorAbs, { force: true });
+            result.removedMirrors++;
+        }
+        catch {
+            /* best-effort cleanup */
+        }
+    }
+    writeConflictIndex(hqRoot, { version: index.version, conflicts: kept });
+    return result;
+}
 //# sourceMappingURL=conflict-index.js.map

package/dist/lib/conflict-index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"conflict-index.js","sourceRoot":"","sources":["../../src/lib/conflict-index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;GAmBG;AAEH,OAAO,KAAK,MAAM,MAAM,QAAQ,CAAC;AACjC,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAG7B,MAAM,aAAa,GAAG,eAAe,CAAC;AACtC,MAAM,cAAc,GAAG,YAAY,CAAC;AAEpC;;GAEG;AACH,MAAM,UAAU,oBAAoB,CAAC,MAAc;IACjD,OAAO,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,aAAa,EAAE,cAAc,CAAC,CAAC;AAC1D,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,iBAAiB,CAAC,MAAc;IAC9C,MAAM,SAAS,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;IAC/C,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC;QAC9B,OAAO,EAAE,OAAO,EAAE,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,CAAC;IACvC,CAAC;IACD,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;IAChD,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAkB,CAAC;IAChD,wEAAwE;IACxE,IAAI,CAAC,MAAM,IAAI,OAAO,MAAM,KAAK,QAAQ,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,CAAC;QAC9E,OAAO,EAAE,OAAO,EAAE,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,CAAC;IACvC,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,kBAAkB,CAChC,MAAc,EACd,KAAoB;IAEpB,MAAM,SAAS,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;IAC/C,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAE3D,MAAM,MAAM,GAAkB;QAC5B,OAAO,EAAE,KAAK,CAAC,OAAO;QACtB,SAAS,EAAE,CAAC,GAAG,KAAK,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC5C,CAAC,CAAC,UAAU,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,CAAC,CACzC;KACF,CAAC;IAEF,2EAA2E;IAC3E,oEAAoE;IACpE,MAAM,OAAO,GAAG,GAAG,SAAS,QAAQ,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;IAC5E,EAAE,CAAC,aAAa,CAAC,OAAO,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;IAC3D,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,SAAS,CAAC,CAAC;AACpC,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,mBAAmB,CACjC,MAAc,EACd,KAAyB;IAEzB,MAAM,KAAK,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAC;IACxC,MAAM,WAAW,GAAG,KAAK,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,KAAK,CAAC,EAAE,CAAC,CAAC;IACxE,IAAI,WAAW,IAAI,CAAC,EAAE,CAAC;QACrB,KAAK,CAAC,SAAS,CAAC,WAAW,CAAC,GAAG,KAAK,CAAC;IACvC,CAAC;SAAM,CAAC;QACN,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAC9B,CAAC;IACD,kBAAkB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;AACpC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,mBAAmB,CAAC,MAAc,EAAE,EAAU;IAC5D,MAAM,KAAK,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAC;IACxC,MAAM,QAAQ,GAAG,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC;IAC5D,IAAI,QAAQ,CAAC,MAAM,KAAK,KAAK,CAAC,SAAS,CAAC,MAAM;QAAE,OAAO;IACvD,kBAAkB,CAAC,MAAM,EAAE,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,CAAC,CAAC;AAC9E,CAAC;AAcD;;;;;;;;;GASG;AACH,SAAS,sBAAsB,CAC7B,KAAa,EACb,KAAe,EACf,KAAa,EACb,KAAe;IAEf,MAAM,KAAK,GAAG,KAAK,CAAC,cAAc,EAAE,CAAC;IACrC,MAAM,KAAK,GAAG,KAAK,CAAC,cAAc,EAAE,CAAC;IACrC,IAAI,KAAK,IAAI,KAAK,EAAE,CAAC;QACnB,IAAI,KAAK,KAAK,KAAK;YAAE,OAAO,KAAK,CAAC;QAClC,OAAO,EAAE,CAAC,YAAY,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC;IAC3D,CAAC;IACD,IAAI,KAAK,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI;QAAE,OAAO,KAAK,CAAC;IAC5C,OAAO,EAAE,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC;AAC/D,CAAC;AAED;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH,MAAM,UAAU,kBAAkB,CAAC,MAAc;IAC/C,MAAM,MAAM,GAA6B;QACvC,aAAa,EAAE,CAAC;QAChB,eAAe,EAAE,CAAC;QAClB,cAAc,EAAE,CAAC;QACjB,IAAI,EAAE,CAAC;KACR,CAAC;IAEF,MAAM,KAAK,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAC;IACxC,IAAI,KAAK,CAAC,SAAS,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,MAAM,CAAC;IAEhD,MAAM,IAAI,GAAyB,EAAE,CAAC;IACtC,MAAM,eAAe,GAAa,EAAE,CAAC;IAErC,KAAK,MAAM,KAAK,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;QACpC,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC,YAAY,CAAC,CAAC;QACxD,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC,YAAY,CAAC,CAAC;QAE1D,IAAI,UAAoB,CAAC;QACzB,IAAI,CAAC;YACH,UAAU,GAAG,EAAE,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC;QACvC,CAAC;QAAC,MAAM,CAAC;YACP,uEAAuE;YACvE,MAAM,CAAC,aAAa,EAAE,CAAC;YACvB,SAAS;QACX,CAAC;QAED,iEAAiE;QACjE,8DAA8D;QAC9D,IAAI,YAAsB,CAAC;QAC3B,IAAI,CAAC;YACH,YAAY,GAAG,EAAE,CAAC,SAAS,CAAC,WAAW,CAAC,CAAC;QAC3C,CAAC;QAAC,MAAM,CAAC;YACP,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YACjB,MAAM,CAAC,IAAI,EAAE,CAAC;YACd,SAAS;QACX,CAAC;QAED,IAAI,SAAkB,CAAC;QACvB,IAAI,CAAC;YACH,SAAS,GAAG,sBAAsB,CAChC,WAAW,EACX,YAAY,EACZ,SAAS,EACT,UAAU,CACX,CAAC;QACJ,CAAC;QAAC,MAAM,CAAC;YACP,oDAAoD;YACpD,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YACjB,MAAM,CAAC,IAAI,EAAE,CAAC;YACd,SAAS;QACX,CAAC;QAED,IAAI,SAAS,EAAE,CAAC;YACd,MAAM,CAAC,eAAe,EAAE,CAAC;YACzB,eAAe,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QAClC,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YACjB,MAAM,CAAC,IAAI,EAAE,CAAC;QAChB,CAAC;IACH,CAAC;IAED,6DAA6D;IAC7D,IAAI,IAAI,CAAC,MAAM,KAAK,KAAK,CAAC,SAAS,CAAC,MAAM;QAAE,OAAO,MAAM,CAAC;IAE1D,6EAA6E;IAC7E,0EAA0E;IAC1E,KAAK,MAAM,SAAS,IAAI,eAAe,EAAE,CAAC;QACxC,IAAI,CAAC;YACH,EAAE,CAAC,MAAM,CAAC,SAAS,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC;YACtC,MAAM,CAAC,cAAc,EAAE,CAAC;QAC1B,CAAC;QAAC,MAAM,CAAC;YACP,yBAAyB;QAC3B,CAAC;IACH,CAAC;IAED,kBAAkB,CAAC,MAAM,EAAE,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IACxE,OAAO,MAAM,CAAC;AAChB,CAAC"}

package/dist/lib/conflict.test.js

@@ -9,7 +9,7 @@ import * as fs from "fs";
 import * as os from "os";
 import * as path from "path";
 import { buildConflictPath, buildConflictId, } from "./conflict-file.js";
-import { appendConflictEntry, getConflictIndexPath, readConflictIndex, removeConflictEntry, writeConflictIndex, } from "./conflict-index.js";
+import { appendConflictEntry, getConflictIndexPath, pruneConflictIndex, readConflictIndex, removeConflictEntry, writeConflictIndex, } from "./conflict-index.js";
 describe("buildConflictPath", () => {
     it("inserts the conflict marker before the original extension", () => {
         expect(buildConflictPath("knowledge/notes.md", "2026-04-27T22:05:14Z", "abc123")).toBe("knowledge/notes.md.conflict-2026-04-27T22-05-14Z-abc123.md");
@@ -105,4 +105,148 @@ describe("conflict index", () => {
         expect(idx.conflicts).toEqual([]);
     });
 });
+describe("pruneConflictIndex", () => {
+    let tmpHq;
+    beforeEach(() => {
+        tmpHq = fs.mkdtempSync(path.join(os.tmpdir(), "hq-cprune-"));
+    });
+    afterEach(() => {
+        fs.rmSync(tmpHq, { recursive: true, force: true });
+    });
+    /** Write a file at a hq-relative path, creating parent dirs. */
+    function put(rel, content) {
+        const abs = path.join(tmpHq, rel);
+        fs.mkdirSync(path.dirname(abs), { recursive: true });
+        fs.writeFileSync(abs, content);
+    }
+    /** Write a symlink at a hq-relative path pointing at `target` (verbatim). */
+    function putLink(rel, target) {
+        const abs = path.join(tmpHq, rel);
+        fs.mkdirSync(path.dirname(abs), { recursive: true });
+        fs.symlinkSync(target, abs);
+    }
+    /**
+     * Build an entry whose original/conflict paths are derived from `id` so each
+     * row addresses distinct files on disk (the shared `entry()` helper above
+     * reuses one fixed path pair, which would collide across rows here).
+     */
+    function rowFor(id) {
+        return {
+            id,
+            originalPath: `dir/${id}.md`,
+            conflictPath: `dir/${id}.md.conflict-2026-04-27T22-05-14Z-abc123.md`,
+            detectedAt: "2026-04-27T22:05:14Z",
+            side: "pull",
+            machineId: "abc123",
+            localHash: "local",
+            remoteHash: "remote",
+        };
+    }
+    it("returns a zeroed result and writes nothing for an empty/absent index", () => {
+        const res = pruneConflictIndex(tmpHq);
+        expect(res).toEqual({
+            prunedOrphans: 0,
+            prunedIdentical: 0,
+            removedMirrors: 0,
+            kept: 0,
+        });
+        expect(fs.existsSync(getConflictIndexPath(tmpHq))).toBe(false);
+    });
+    it("drops a row whose .conflict-* mirror no longer exists (orphan)", () => {
+        const row = rowFor("orphan");
+        put(row.originalPath, "still here");
+        // No mirror file on disk.
+        writeConflictIndex(tmpHq, { version: 1, conflicts: [row] });
+        const res = pruneConflictIndex(tmpHq);
+        expect(res.prunedOrphans).toBe(1);
+        expect(res.kept).toBe(0);
+        expect(readConflictIndex(tmpHq).conflicts).toHaveLength(0);
+    });
+    it("drops a byte-identical row and deletes its mirror file", () => {
+        const row = rowFor("identical");
+        put(row.originalPath, "same bytes");
+        put(row.conflictPath, "same bytes");
+        writeConflictIndex(tmpHq, { version: 1, conflicts: [row] });
+        const res = pruneConflictIndex(tmpHq);
+        expect(res.prunedIdentical).toBe(1);
+        expect(res.removedMirrors).toBe(1);
+        expect(readConflictIndex(tmpHq).conflicts).toHaveLength(0);
+        expect(fs.existsSync(path.join(tmpHq, row.conflictPath))).toBe(false);
+        // The user's original is never touched.
+        expect(fs.existsSync(path.join(tmpHq, row.originalPath))).toBe(true);
+    });
+    it("keeps a genuinely divergent row and leaves both files in place", () => {
+        const row = rowFor("real");
+        put(row.originalPath, "local edit");
+        put(row.conflictPath, "remote edit");
+        writeConflictIndex(tmpHq, { version: 1, conflicts: [row] });
+        const res = pruneConflictIndex(tmpHq);
+        expect(res.kept).toBe(1);
+        expect(res.prunedIdentical).toBe(0);
+        expect(res.prunedOrphans).toBe(0);
+        expect(readConflictIndex(tmpHq).conflicts.map((c) => c.id)).toEqual(["real"]);
+        expect(fs.existsSync(path.join(tmpHq, row.conflictPath))).toBe(true);
+    });
+    it("keeps a row whose original is missing (local-delete divergence)", () => {
+        const row = rowFor("deleted-local");
+        // No original; mirror present.
+        put(row.conflictPath, "remote bytes");
+        writeConflictIndex(tmpHq, { version: 1, conflicts: [row] });
+        const res = pruneConflictIndex(tmpHq);
+        expect(res.kept).toBe(1);
+        expect(readConflictIndex(tmpHq).conflicts).toHaveLength(1);
+    });
+    it("treats two symlinks with the same target as identical, differing targets as a conflict", () => {
+        const same = rowFor("link-same");
+        putLink(same.originalPath, "../target/a");
+        putLink(same.conflictPath, "../target/a");
+        const diff = rowFor("link-diff");
+        putLink(diff.originalPath, "../target/a");
+        putLink(diff.conflictPath, "../target/b");
+        writeConflictIndex(tmpHq, { version: 1, conflicts: [same, diff] });
+        const res = pruneConflictIndex(tmpHq);
+        expect(res.prunedIdentical).toBe(1);
+        expect(res.kept).toBe(1);
+        expect(readConflictIndex(tmpHq).conflicts.map((c) => c.id)).toEqual([
+            "link-diff",
+        ]);
+    });
+    it("partitions a mixed batch and preserves only the real conflicts", () => {
+        const orphan = rowFor("orphan");
+        put(orphan.originalPath, "x"); // mirror missing
+        const identical = rowFor("identical");
+        put(identical.originalPath, "dup");
+        put(identical.conflictPath, "dup");
+        const real = rowFor("real");
+        put(real.originalPath, "L");
+        put(real.conflictPath, "R");
+        writeConflictIndex(tmpHq, {
+            version: 1,
+            conflicts: [orphan, identical, real],
+        });
+        const res = pruneConflictIndex(tmpHq);
+        expect(res).toEqual({
+            prunedOrphans: 1,
+            prunedIdentical: 1,
+            removedMirrors: 1,
+            kept: 1,
+        });
+        expect(readConflictIndex(tmpHq).conflicts.map((c) => c.id)).toEqual(["real"]);
+    });
+    it("does not rewrite the index file when nothing is pruned", () => {
+        const real = rowFor("real");
+        put(real.originalPath, "L");
+        put(real.conflictPath, "R");
+        writeConflictIndex(tmpHq, { version: 1, conflicts: [real] });
+        const indexPath = getConflictIndexPath(tmpHq);
+        const before = fs.statSync(indexPath).mtimeMs;
+        // Advance the clock past filesystem mtime granularity, then prune.
+        const spin = Date.now() + 20;
+        while (Date.now() < spin) {
+            /* busy-wait ~20ms so a rewrite would move mtime */
+        }
+        pruneConflictIndex(tmpHq);
+        expect(fs.statSync(indexPath).mtimeMs).toBe(before);
+    });
+});
 //# sourceMappingURL=conflict.test.js.map

package/dist/lib/conflict.test.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@indigoai-us/hq-cloud",
-  "version": "6.1.0",
+  "version": "6.2.0",
   "description": "HQ by Indigo cloud sync engine — bidirectional S3 sync for mobile access",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

package/src/bin/sync-runner.ts

@@ -99,6 +99,7 @@ import {
 import { collectAndSendTelemetry } from "../telemetry.js";
 import { collectAndSendSkillTelemetry } from "../skill-telemetry.js";
 import { reindexAfterSync } from "../qmd-reindex.js";
+import { pruneConflictIndex } from "../lib/conflict-index.js";
 import { describeError } from "../lib/describe-error.js";
 import { getOrCreateMachineId } from "../lib/machine-id.js";
 import {
@@ -1639,6 +1640,23 @@ export async function runRunner(
     }
   }
 
+  // Post-sync conflict-ledger prune — also a best-effort tail step (runs AFTER
+  // `all-complete`, never touches the exit code). The producers only append a
+  // conflict row after proving real divergence, but the ledger has no other
+  // self-healing path: rows for byte-identical false positives (legacy or
+  // since-reverted) and orphaned `.conflict-*` mirrors otherwise linger
+  // forever and make `.hq-conflicts/index.json` over-report. One GC pass per
+  // run keeps it converged. Idempotent and cheap on a clean ledger (a no-row
+  // index returns immediately and never rewrites the file). Opt-out via
+  // HQ_CONFLICT_PRUNE_ON_SYNC=0.
+  if (process.env.HQ_CONFLICT_PRUNE_ON_SYNC !== "0") {
+    try {
+      pruneConflictIndex(parsed.hqRoot);
+    } catch {
+      // Defensive: a prune failure must never affect the sync outcome.
+    }
+  }
+
   // Exit 2 only when something actually threw (`errors.length > 0`). A clean
   // conflict-abort sets `partial: true` in the JSON but exits 0 — the Tauri
   // menubar's non-zero-exit Sentry capture would otherwise fire for normal

package/src/cli/index.ts

@@ -26,10 +26,10 @@ export type { PromoteOptions, PromoteResult } from "./promote.js";
 
 // Skill/personal-overlay mirroring + workers-registry regen (formerly the
 // hq-core master-sync.sh hook; `hq reindex`).
-export { reindex, reindexScriptPath } from "./reindex.js";
+export { reindex } from "./reindex.js";
 export type { ReindexOptions, ReindexResult } from "./reindex.js";
 
 // Drift-preserving HQ-core re-sync (formerly bundled only inside the HQ Sync
 // menubar app). Now shared between the app and `hq rescue`.
-export { rescue, rescueScriptPath, buildRescueArgs } from "./rescue.js";
+export { rescue, buildRescueArgs } from "./rescue.js";
 export type { RescueOptions, RescueResult } from "./rescue.js";

package/src/cli/reindex.test.ts

@@ -2,25 +2,17 @@
  * Unit tests for `hq reindex` (the formerly-bash hq-core hook, now shipped
  * in this package and invoked via the CLI).
  *
- * The logic itself lives in scripts/reindex.sh; these tests exercise it via
- * the reindex() wrapper against a temp HQ tree, asserting the observable
+ * The logic is implemented natively in TypeScript in ./reindex.ts; these tests
+ * exercise reindex() directly against a temp HQ tree, asserting the observable
  * filesystem outcomes (skill wrappers, personal-overlay mirroring) rather than
- * re-deriving the bash internals.
+ * re-deriving the implementation internals.
  */
 
 import { describe, it, expect, beforeEach, afterEach } from "vitest";
 import * as fs from "fs";
 import * as path from "path";
 import * as os from "os";
-import { reindex, reindexScriptPath } from "./reindex.js";
-
-describe("reindexScriptPath", () => {
-  it("resolves to the bundled script and the file exists", () => {
-    const p = reindexScriptPath();
-    expect(p.endsWith(path.join("scripts", "reindex.sh"))).toBe(true);
-    expect(fs.existsSync(p)).toBe(true);
-  });
-});
+import { reindex } from "./reindex.js";
 
 describe("reindex", () => {
   let root: string;
@@ -91,4 +83,45 @@ describe("reindex", () => {
       fs.readlinkSync(path.join(root, ".claude/skills/core:demo/SKILL.md")),
     ).toBe("../../../core/skills/demo/SKILL.md");
   });
+
+  it("skips `_`-prefixed and dotfile skill folders", () => {
+    writeSkill("core/skills/_template");
+    fs.mkdirSync(path.join(root, "core/skills/.hidden"), { recursive: true });
+    fs.writeFileSync(path.join(root, "core/skills/.hidden/SKILL.md"), "x\n");
+    writeSkill("core/skills/real");
+
+    reindex({ repoRoot: root });
+
+    expect(fs.existsSync(path.join(root, ".claude/skills/core:real"))).toBe(true);
+    expect(fs.existsSync(path.join(root, ".claude/skills/core:_template"))).toBe(false);
+    expect(fs.existsSync(path.join(root, ".claude/skills/core:.hidden"))).toBe(false);
+  });
+
+  it("removes legacy .claude/commands/<ns>/<skill>.md bridge symlinks", () => {
+    const cmdDir = path.join(root, ".claude/commands/core");
+    fs.mkdirSync(cmdDir, { recursive: true });
+    // Legacy bridge symlink (matches the cleanup pattern) → removed.
+    fs.symlinkSync("../../../core/skills/demo/SKILL.md", path.join(cmdDir, "demo.md"));
+    // A real file (non-symlink) → preserved.
+    fs.writeFileSync(path.join(cmdDir, "keep.md"), "manual\n");
+
+    reindex({ repoRoot: root });
+
+    expect(fs.existsSync(path.join(cmdDir, "demo.md"))).toBe(false);
+    expect(fs.existsSync(path.join(cmdDir, "keep.md"))).toBe(true);
+  });
+
+  it("leaves hand-authored composite wrappers (unmanaged namespace) alone", () => {
+    // A wrapper whose namespace ('vendor') is not a managed namespace and
+    // whose target points into core/skills/<other> — must not be pruned.
+    const wrapper = path.join(root, ".claude/skills/vendor:tool");
+    fs.mkdirSync(wrapper, { recursive: true });
+    writeSkill("core/skills/helper");
+    fs.symlinkSync("../../../core/skills/helper/SKILL.md", path.join(wrapper, "SKILL.md"));
+
+    reindex({ repoRoot: root });
+
+    expect(fs.existsSync(wrapper)).toBe(true);
+    expect(fs.lstatSync(path.join(wrapper, "SKILL.md")).isSymbolicLink()).toBe(true);
+  });
 });