skillwiki 0.10.114 → 0.10.116

package/dist/{chunk-5RHR4FEK.js → chunk-WV7NLVCD.js}

@@ -48,7 +48,7 @@ import {
   satelliteGateFromFleetLoad,
   snapshotterAliasForLocalHost,
   toUndirectedWeighted
-} from "./chunk-FQERKMD7.js";
+} from "./chunk-CNELLIZ2.js";
 import {
   eventPathFor,
   writeLogEvent
@@ -71,12 +71,6 @@ import {
   mergeMcpAuthIntoEnv,
   redactMcpSecret
 } from "./chunk-OGEAFXON.js";
-import {
-  xml
-} from "./chunk-XJ5VEIH7.js";
-import {
-  atomicWriteText
-} from "./chunk-6VUK2FTX.js";
 import {
   CLIP_NOT_CONFIGURED,
   PRODUCTION_MIRROR_LABEL,
@@ -94,6 +88,9 @@ import {
   resolveSkillwikiHome,
   writeDotenv
 } from "./chunk-IJKJGQKL.js";
+import {
+  atomicWriteText
+} from "./chunk-6VUK2FTX.js";
 import {
   CompoundSchema,
   ExitCode,
@@ -4423,8 +4420,8 @@ var mcpHandshakeProbe = {
 };
 
 // src/doctor/probes/clip-outbox.ts
-import { existsSync as existsSync18, readFileSync as readFileSync12 } from "fs";
-import { execSync as execSync7 } from "child_process";
+import { existsSync as existsSync18 } from "fs";
+import { execSync as execSync7, execFileSync } from "child_process";
 import { platform as platform6 } from "os";
 import { join as join21 } from "path";
 var CLIP_CHECK_IDS = [
@@ -4477,6 +4474,27 @@ function launchdLoaded(label) {
     return false;
   }
 }
+function validateClipLaunchdPlist(value, label, command, root) {
+  if (!value || typeof value !== "object" || Array.isArray(value)) return false;
+  const plist = value;
+  const args = plist.ProgramArguments;
+  if (plist.Label !== label || !Array.isArray(args) || args.length < 4 || !args.every((arg) => typeof arg === "string") || !args[0] || args[2] !== "clip-outbox" || args[3] !== command) return false;
+  return root === void 0 ? plist.WatchPaths === void 0 : Array.isArray(plist.WatchPaths) && plist.WatchPaths.length === 1 && plist.WatchPaths[0] === root;
+}
+function launchdExplicitlyDisabled(text, label) {
+  return text.split("\n").some((line) => {
+    const match = line.trim().match(/^"([^"]+)"\s*=>\s*(true|false|enabled|disabled)\s*;?$/);
+    return match?.[1] === label && (match[2] === "true" || match[2] === "disabled");
+  });
+}
+function validInstalledPlist(path, label, command, root) {
+  const decoded = JSON.parse(execFileSync("/usr/bin/plutil", ["-convert", "json", "-o", "-", path], {
+    encoding: "utf8",
+    timeout: 2e3,
+    stdio: ["ignore", "pipe", "ignore"]
+  }));
+  return validateClipLaunchdPlist(decoded, label, command, root);
+}
 function watcherStatus(env, label, home, root) {
   const fixture = env.CLIP_WATCHER_FIXTURE;
   if (fixture === "loaded-enabled") return { loaded: true, enabled: true, kind: "production" };
@@ -4491,11 +4509,9 @@ function watcherStatus(env, label, home, root) {
   }
   const plist = join21(home, "Library", "LaunchAgents", `${label}.plist`);
   try {
-    const text = readFileSync12(plist, "utf8");
-    const xmlRoot = xml(root);
-    const matchesRoot = text.includes(`<key>WatchPaths</key><array><string>${xmlRoot}</string></array>`);
+    const matchesRoot = validInstalledPlist(plist, label, "watch", root);
     const disabled = execSync7(`launchctl print-disabled gui/${process.getuid()}`, { encoding: "utf8", timeout: 2e3, stdio: ["ignore", "pipe", "ignore"] });
-    const explicitlyDisabled = disabled.split("\n").some((line) => line.includes(`"${label}"`) && line.includes("true"));
+    const explicitlyDisabled = launchdExplicitlyDisabled(disabled, label);
     return { loaded: true, enabled: matchesRoot && !explicitlyDisabled, kind: "production" };
   } catch {
     return { loaded: true, enabled: false, kind: "unknown" };
@@ -4518,11 +4534,9 @@ function listenerOk(env, home) {
   if (!launchdLoaded(PRODUCTION_MIRROR_LABEL)) return false;
   const plist = join21(home, "Library", "LaunchAgents", `${PRODUCTION_MIRROR_LABEL}.plist`);
   try {
-    const text = readFileSync12(plist, "utf8");
-    if (text.includes("<key>WatchPaths</key>")) return false;
+    const valid = validInstalledPlist(plist, PRODUCTION_MIRROR_LABEL, "mirror-watch");
     const disabled = execSync7(`launchctl print-disabled gui/${process.getuid()}`, { encoding: "utf8", timeout: 2e3, stdio: ["ignore", "pipe", "ignore"] });
-    const explicitlyDisabled = disabled.split("\n").some((line) => line.includes(`"${PRODUCTION_MIRROR_LABEL}"`) && line.includes("true"));
-    return text.includes("mirror-watch") && text.includes(PRODUCTION_MIRROR_LABEL) && !explicitlyDisabled;
+    return valid && !launchdExplicitlyDisabled(disabled, PRODUCTION_MIRROR_LABEL);
   } catch {
     return false;
   }
@@ -4701,7 +4715,7 @@ async function runDoctor(input) {
 }
 
 // src/utils/package-info.ts
-import { readFileSync as readFileSync13 } from "fs";
+import { readFileSync as readFileSync12 } from "fs";
 function packageJsonCandidateUrls(baseUrl = import.meta.url) {
   return [
     new URL("../package.json", baseUrl),
@@ -4711,7 +4725,7 @@ function packageJsonCandidateUrls(baseUrl = import.meta.url) {
 function readCliPackageJson(baseUrl = import.meta.url) {
   for (const url of packageJsonCandidateUrls(baseUrl)) {
     try {
-      const pkg = JSON.parse(readFileSync13(url, "utf8"));
+      const pkg = JSON.parse(readFileSync12(url, "utf8"));
       if (typeof pkg.version === "string") {
         return { ...pkg, version: pkg.version };
       }
@@ -4722,8 +4736,8 @@ function readCliPackageJson(baseUrl = import.meta.url) {
 }
 
 // src/utils/vault-write-gates.ts
-import { execFileSync } from "child_process";
-import { existsSync as existsSync20, readdirSync as readdirSync7, readFileSync as readFileSync14, statSync as statSync3 } from "fs";
+import { execFileSync as execFileSync2 } from "child_process";
+import { existsSync as existsSync20, readdirSync as readdirSync7, readFileSync as readFileSync13, statSync as statSync3 } from "fs";
 import { join as join22, relative as relative2 } from "path";
 var DEFAULT_DIRTY_VOLUME_THRESHOLD = 50;
 var DEFAULT_CAPTURE_BUDGET = 20;
@@ -4805,7 +4819,7 @@ function measureDirtyVolume(vault) {
   }
   let porcelain = "";
   try {
-    porcelain = execFileSync("git", ["status", "--porcelain"], {
+    porcelain = execFileSync2("git", ["status", "--porcelain"], {
       cwd: vault,
       encoding: "utf8",
       stdio: ["pipe", "pipe", "pipe"]
@@ -4996,7 +5010,7 @@ function listProjectDayCaptures(vault, project, day) {
     }
     if (norm.startsWith("raw/transcripts/")) {
       try {
-        const body = readFileSync14(abs, "utf8");
+        const body = readFileSync13(abs, "utf8");
         if (body.includes(`project: ${slug}`) || body.includes(`project: "[[${slug}]]"`) || body.includes(`project: [[${slug}]]`)) {
           found.push(norm);
         } else if (base.includes(slug)) {

package/dist/cli.js

@@ -1,4 +1,8 @@
 #!/usr/bin/env node
+import {
+  CLIP_MIGRATION_HINT,
+  refreshInstalledClipPlist
+} from "./chunk-4ZKCGX4V.js";
 import {
   buildDeleteIntent,
   normalizeVaultRelPath,
@@ -64,7 +68,7 @@ import {
   upsertIndexEntry,
   vectorIndexStatus,
   withMcpClient
-} from "./chunk-5RHR4FEK.js";
+} from "./chunk-WV7NLVCD.js";
 import {
   applySourceDisposition,
   decodeSourceActionApproval,
@@ -174,7 +178,7 @@ import {
   stageVaultContentChanges,
   supersedeStaleReviewRequiredJournals,
   taxonomyCommentForPage
-} from "./chunk-FQERKMD7.js";
+} from "./chunk-CNELLIZ2.js";
 import {
   authorizeRawOperation,
   buildSourceReferenceIndex,
@@ -217,13 +221,6 @@ import {
   nonEmptyEnvValue,
   redactMcpSecret
 } from "./chunk-OGEAFXON.js";
-import {
-  CLIP_MIGRATION_HINT,
-  refreshInstalledClipPlist
-} from "./chunk-XJ5VEIH7.js";
-import {
-  atomicWriteText
-} from "./chunk-6VUK2FTX.js";
 import {
   CLIP_NOT_CONFIGURED,
   loadClipOutboxConfig
@@ -239,6 +236,9 @@ import {
   resolveSkillwikiHome,
   writeDotenv
 } from "./chunk-IJKJGQKL.js";
+import {
+  atomicWriteText
+} from "./chunk-6VUK2FTX.js";
 import {
   ExitCode,
   MetaSchema,
@@ -3608,7 +3608,7 @@ async function runClipOutboxStatus(home) {
 }
 async function runClipOutboxInstall(input) {
   try {
-    const { migrateClipOutbox } = await import("./migrate-SRRCXI2K.js");
+    const { migrateClipOutbox } = await import("./migrate-4K6SXESR.js");
     return { exitCode: ExitCode.OK, result: ok(await migrateClipOutbox(input)) };
   } catch (e) {
     return { exitCode: ExitCode.PREFLIGHT_FAILED, result: err("PREFLIGHT_FAILED", { message: e instanceof Error ? e.message : "clip migration failed" }) };
@@ -3624,7 +3624,7 @@ async function runClipOutboxWatch(home) {
     const { loadClipCredentials, validateRuntime } = await import("./runtime-LQZIG3XN.js");
     const { createS3CreateOnlyPut, parseDestination } = await import("./upload-HTE62TOV.js");
     const { postReadyHint } = await import("./ready-S7F53Q2D.js");
-    const { startClipWorker } = await import("./watcher-VJ3TOU6J.js");
+    const { startClipWorker } = await import("./watcher-2PBZQLKL.js");
     const cfg = resolved.config;
     const credentials = await loadClipCredentials(home, cfg);
     await validateRuntime(home, cfg, credentials.s3.endpoint);
@@ -11715,7 +11715,7 @@ async function emitManagedVaultWrite(vault, command, mutate, opts) {
   if (dirty) {
     return emit(dirty, void 0, { postCommit: false });
   }
-  const { runManagedWriteTransaction: runManagedWriteTransaction2 } = await import("./managed-write-preflight-2BMHZWVJ.js");
+  const { runManagedWriteTransaction: runManagedWriteTransaction2 } = await import("./managed-write-preflight-KCQHTIHI.js");
   const run = await runManagedWriteTransaction2({
     vault,
     command,

package/dist/{managed-write-preflight-2BMHZWVJ.js → managed-write-preflight-KCQHTIHI.js}

@@ -6,12 +6,12 @@ import {
   runManagedWritePeerGate,
   runManagedWritePreflight,
   runManagedWriteTransaction
-} from "./chunk-FQERKMD7.js";
+} from "./chunk-CNELLIZ2.js";
 import "./chunk-K3YZESND.js";
 import "./chunk-3TKNAOJH.js";
 import "./chunk-JL2SCLXT.js";
-import "./chunk-6VUK2FTX.js";
 import "./chunk-IJKJGQKL.js";
+import "./chunk-6VUK2FTX.js";
 import "./chunk-VNSZCK5V.js";
 export {
   DEFAULT_MANAGED_WRITE_WAIT_MS,

package/dist/{migrate-SRRCXI2K.js → migrate-4K6SXESR.js}

@@ -6,11 +6,11 @@ import {
   refreshInstalledClipPlist,
   stableCliBinary,
   xml
-} from "./chunk-XJ5VEIH7.js";
-import "./chunk-6VUK2FTX.js";
+} from "./chunk-4ZKCGX4V.js";
 import "./chunk-OWWWO2XS.js";
 import "./chunk-5D5HFQ76.js";
 import "./chunk-IJKJGQKL.js";
+import "./chunk-6VUK2FTX.js";
 import "./chunk-VNSZCK5V.js";
 export {
   CLIP_MIGRATION_HINT,

package/dist/skillwiki-mcp.js

@@ -1,20 +1,19 @@
 #!/usr/bin/env node
 import {
   runSkillwikiMcpStdio
-} from "./chunk-5RHR4FEK.js";
+} from "./chunk-WV7NLVCD.js";
 import "./chunk-CBT35FAW.js";
 import "./chunk-7I2TPIV5.js";
 import "./chunk-IJWZDQDH.js";
-import "./chunk-FQERKMD7.js";
+import "./chunk-CNELLIZ2.js";
 import "./chunk-K3YZESND.js";
 import "./chunk-3TKNAOJH.js";
 import "./chunk-JL2SCLXT.js";
 import "./chunk-OGEAFXON.js";
-import "./chunk-XJ5VEIH7.js";
-import "./chunk-6VUK2FTX.js";
 import "./chunk-OWWWO2XS.js";
 import "./chunk-5D5HFQ76.js";
 import "./chunk-IJKJGQKL.js";
+import "./chunk-6VUK2FTX.js";
 import "./chunk-VNSZCK5V.js";
 
 // src/mcp-entry.ts

package/dist/vault-sync/scripts/lib/deploy-runtime.py

@@ -0,0 +1,126 @@
+#!/usr/bin/env python3
+"""Upgrade installed helpers without touching configuration or scheduler state.
+
+Each entry point execs an immutable payload path, so an in-flight helper and
+its late-loaded libraries stay on the same release across subsequent upgrades.
+Legacy directory migration refuses while an installed helper is running.
+"""
+import datetime
+import hashlib
+import json
+import os
+from pathlib import Path
+import shutil
+import signal
+import subprocess
+import sys
+import tempfile
+
+
+def deploy(root, share, role, version, commit, host, dry_run=False):
+    root, share = Path(root).resolve(), Path(share).resolve()
+    current = share / "bin"
+    if not current.is_dir() or not (share / "runtime-manifest.json").is_file():
+        raise ValueError("runtime-only requires an existing installation and manifest")
+    if dry_run:
+        print("runtime-only: stage immutable payload, validate, back up and switch bin; preserve configuration and scheduler")
+        return
+    lock = share / ".runtime-upgrade.lock"
+    lock.mkdir()  # No age-based reclamation of another deployer's lock.
+    release = None
+    backup = None
+    swapped = False
+    old_link = os.readlink(current) if current.is_symlink() else None
+    manifest = share / "runtime-manifest.json"
+    old_manifest = manifest.read_bytes()
+    try:
+        # Existing old-style entry points cannot pin their late-loaded libs.
+        # Refuse migration until they finish; never stop or start a content job.
+        processes = subprocess.check_output(["ps", "-axww", "-o", "args="], text=True)
+        if not current.is_symlink() and any(str(current) + "/" in line for line in processes.splitlines()):
+            raise ValueError("installed helper is active; retry runtime upgrade after it exits")
+        releases = share / "runtime-releases"
+        releases.mkdir(exist_ok=True)
+        release = Path(tempfile.mkdtemp(prefix="runtime-", dir=releases))
+        payload = release / "payload"
+        shutil.copytree(root / "scripts", payload, ignore=shutil.ignore_patterns("__pycache__", "*.pyc"))
+        shutil.copy2(root / "skills/vault-presync/wiki-sync.sh", payload / "wiki-sync.sh")
+        # Keep auxiliary installed files while replacing package-owned helpers.
+        for source in current.iterdir():
+            if source.name in ("lib", "payload", "runtime-manifest.json", "previous-runtime-manifest.json"):
+                continue
+            if source.is_file():
+                shutil.copy2(source, release / source.name)
+        shutil.copytree(payload / "lib", release / "lib")
+        for file in payload.rglob("*"):
+            if file.suffix == ".sh":
+                subprocess.run(["bash", "-n", str(file)], check=True)
+            elif file.suffix == ".py":
+                compile(file.read_bytes(), str(file), "exec")
+        for file in payload.glob("*.sh"):
+            file.chmod(0o755)
+            # Quote absolute immutable path using shell single-quote escaping.
+            quoted = "'" + str(file).replace("'", "'\\''") + "'"
+            launcher = release / file.name
+            launcher.write_text("#!/bin/sh\nexec /bin/bash " + quoted + ' "$@"\n')
+            launcher.chmod(0o755)
+        files = {"bin/" + str(p.relative_to(release)): hashlib.sha256(p.read_bytes()).hexdigest()
+                 for p in sorted(release.rglob("*")) if p.is_file()}
+        agents = Path.home() / "Library/LaunchAgents"
+        for p in sorted(agents.glob("com.karlchow.wiki-*.plist")):
+            files["LaunchAgents/" + p.name] = hashlib.sha256(p.read_bytes()).hexdigest()
+        new_manifest = dict(schema_version=1, package_version=version, package_commit=commit,
+                            installer_version=version, installed_at=datetime.datetime.now(datetime.timezone.utc).isoformat(),
+                            role=role, host_id=host, files=files)
+        (release / "runtime-manifest.json").write_text(json.dumps(new_manifest, indent=2) + "\n")
+        (release / "previous-runtime-manifest.json").write_bytes(old_manifest)
+        if os.environ.get("VS_RUNTIME_TEST_FAIL") == "before-switch":
+            raise ValueError("injected pre-switch failure")
+        candidate = share / ".bin-next"
+        candidate.symlink_to(release)
+        if old_link is None:
+            backup = share / ("bin-backup-" + release.name)
+            current.rename(backup)
+            # A legacy runner that opened its script during staging must finish
+            # against the old libraries; refuse before exposing new libraries.
+            processes = subprocess.check_output(["ps", "-axww", "-o", "args="], text=True)
+            if any(str(current) + "/" in line for line in processes.splitlines()):
+                raise ValueError("legacy helper started during staging; runtime restored, retry later")
+        os.replace(candidate, current)
+        swapped = True
+        if os.environ.get("VS_RUNTIME_TEST_FAIL") == "after-switch":
+            raise ValueError("injected post-switch failure")
+        staged_manifest = share / ".runtime-manifest-next.json"
+        staged_manifest.write_bytes((release / "runtime-manifest.json").read_bytes())
+        os.replace(staged_manifest, manifest)
+        for relative, digest in files.items():
+            if relative.startswith("bin/") and hashlib.sha256((share / relative).read_bytes()).hexdigest() != digest:
+                raise ValueError("installed runtime hash mismatch")
+        print("runtime-only installed " + version + "; rollback=" + str(backup or old_link))
+    except BaseException:
+        if swapped:
+            current.unlink()
+        if backup is not None and backup.exists():
+            backup.rename(current)
+        elif swapped and old_link is not None:
+            current.symlink_to(old_link)
+        manifest.write_bytes(old_manifest)
+        if release is not None:
+            shutil.rmtree(release)
+        raise
+    finally:
+        (share / ".bin-next").unlink(missing_ok=True)
+        (share / ".runtime-manifest-next.json").unlink(missing_ok=True)
+        lock.rmdir()
+
+
+if __name__ == "__main__":
+    def interrupted(_signal, _frame):
+        raise KeyboardInterrupt("runtime upgrade interrupted")
+    signal.signal(signal.SIGTERM, interrupted)
+    signal.signal(signal.SIGINT, interrupted)
+    try:
+        deploy(*sys.argv[1:7], dry_run=sys.argv[7:] == ["--dry-run"])
+    except (OSError, ValueError, subprocess.SubprocessError) as error:
+        print("runtime-only refused: " + str(error), file=sys.stderr)
+        sys.exit(1)

package/dist/vault-sync/scripts/lib/git-operation-journal.sh

@@ -456,67 +456,13 @@ vault_sync_op_write_inventory() {
 # Fail closed on any mismatch.
 vault_sync_op_verify_inventory() {
   local repo="$1" op_id="$2" stash_oid="${3:-}" skip_content_paths="${4:-}"
-  local inv section path expected_hash actual_hash unmerged skip has_u3
-
+  local inv restore_head helper
   inv="$(vault_sync_op_get_field "$repo" "$op_id" inventory_path)" || return 1
-  [ -f "$inv" ] || return 1
-
-  unmerged="$(git -C "$repo" diff --name-only --diff-filter=U 2>/dev/null || true)"
-  has_u3=0
-  if [ -n "$stash_oid" ] && git -C "$repo" rev-parse -q --verify "${stash_oid}^3" >/dev/null 2>&1; then
-    has_u3=1
-  fi
-  section=""
-  while IFS= read -r path || [ -n "$path" ]; do
-    case "$path" in
-      "# staged") section="staged"; continue ;;
-      "# tracked") section="tracked"; continue ;;
-      "# untracked") section="untracked"; continue ;;
-      ""|\#*) continue ;;
-    esac
-    [ -n "$path" ] || continue
-    [ -n "$section" ] || continue
-
-    # Skip content checks for currently-unmerged conflict paths.
-    if printf '%s\n' "$unmerged" | grep -Fxq -- "$path"; then
-      continue
-    fi
-
-    skip=0
-    if [ -n "$skip_content_paths" ] && printf '%s\n' "$skip_content_paths" | grep -Fxq -- "$path"; then
-      skip=1
-    fi
-
-    case "$section" in
-      staged|tracked)
-        if [ -n "$stash_oid" ] && git -C "$repo" cat-file -e "$stash_oid:$path" 2>/dev/null; then
-          if [ ! -f "$repo/$path" ] && [ ! -L "$repo/$path" ]; then
-            return 1
-          fi
-          if [ "$skip" -eq 0 ]; then
-            expected_hash="$(git -C "$repo" rev-parse "$stash_oid:$path" 2>/dev/null || echo missing)"
-            actual_hash="$(git -C "$repo" hash-object -- "$repo/$path" 2>/dev/null || echo missing)"
-            [ "$expected_hash" = "$actual_hash" ] || return 1
-          fi
-        fi
-        ;;
-      untracked)
-        if [ ! -e "$repo/$path" ] && [ ! -L "$repo/$path" ]; then
-          return 1
-        fi
-        if [ "$skip" -eq 0 ] && [ "$has_u3" -eq 1 ]; then
-          if git -C "$repo" cat-file -e "${stash_oid}^3:$path" 2>/dev/null; then
-            expected_hash="$(git -C "$repo" rev-parse "${stash_oid}^3:$path" 2>/dev/null || echo missing)"
-            if [ -f "$repo/$path" ]; then
-              actual_hash="$(git -C "$repo" hash-object -- "$repo/$path" 2>/dev/null || echo missing)"
-              [ "$expected_hash" = "$actual_hash" ] || return 1
-            fi
-          fi
-        fi
-        ;;
-    esac
-  done <"$inv"
-  return 0
+  [ -f "$inv" ] && [ -n "$stash_oid" ] || return 1
+  restore_head="$(vault_sync_op_get_field "$repo" "$op_id" restore_head)"
+  [ -n "$restore_head" ] || restore_head="$(git -C "$repo" rev-parse HEAD)" || return 1
+  helper="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/verify-stash-inventory.py"
+  python3 "$helper" "$repo" "$inv" "$stash_oid" "$restore_head" "$skip_content_paths"
 }
 
 vault_sync_op_stash_push_owned() {

package/dist/vault-sync/scripts/lib/runtime-manifest.sh

@@ -99,6 +99,14 @@ vault_sync_package_commit() {
     printf '%s\n' "$_override"
     return 0
   fi
+  # Exported deployment bundles have no .git; the bundle pin is the exact commit.
+  if [ -f "$_root/../../.deploy-pin" ]; then
+    _pin="$(cat "$_root/../../.deploy-pin")"
+    if printf '%s\n' "$_pin" | LC_ALL=C grep -Eq '^[0-9a-f]{40,64}$'; then
+      printf '%s\n' "$_pin"
+      return 0
+    fi
+  fi
   if command -v git >/dev/null 2>&1 && [ -d "$_root/../../.git" -o -f "$_root/../../.git" ] 2>/dev/null; then
     git -C "$_root/../.." rev-parse HEAD 2>/dev/null || echo ""
     return 0

package/dist/vault-sync/scripts/lib/verify-stash-inventory.py

@@ -0,0 +1,105 @@
+#!/usr/bin/env python3
+"""Verify an owned stash restore against its frozen post-rebase baseline."""
+import os
+import pathlib
+import subprocess
+import sys
+import tempfile
+
+
+def verify(repo, inventory, stash, head, skipped):
+    def git(*args, data=None, stream=None):
+        return subprocess.run(["git", "--literal-pathspecs", "-C", repo, *args], input=data, stdin=stream,
+                              stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True).stdout
+
+    def entry(tree, path):
+        raw = git("ls-tree", "-z", tree, "--", path)
+        if not raw:
+            return None
+        meta, name = raw.rstrip(b"\0").split(b"\t", 1)
+        mode, kind, oid = meta.decode().split()
+        if name.decode() != path or kind != "blob":
+            raise ValueError("unsupported inventory entry")
+        return mode, oid
+
+    def expected(path):
+        base, local, upstream = (entry(tree, path) for tree in (stash + "^1", stash, head))
+        if local == base:
+            return upstream
+        if upstream == base or local == upstream:
+            return local
+        if not base or not local or not upstream:
+            raise ValueError("ambiguous add/delete restore")
+        if any(mode not in ("100644", "100755") for mode, _ in (base, local, upstream)):
+            raise ValueError("ambiguous file-type restore")
+        mode = local[0] if upstream[0] == base[0] else upstream[0]
+        with tempfile.TemporaryDirectory(prefix="stash-merge-") as directory:
+            files = [pathlib.Path(directory, name) for name in ("upstream", "base", "local")]
+            for file, value in zip(files, (upstream, base, local)):
+                if int(git("cat-file", "-s", value[1])) > 16 * 1024 * 1024:
+                    raise ValueError("merge verification exceeds bounded file size")
+                file.write_bytes(git("cat-file", "blob", value[1]))
+            merged = subprocess.run(["git", "merge-file", "-p", *map(str, files)],
+                                    stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            if merged.returncode:
+                raise ValueError("ambiguous content restore")
+            return mode, git("hash-object", "--stdin", data=merged.stdout).decode().strip()
+
+    if git("rev-parse", "HEAD").strip() != git("rev-parse", head).strip():
+        raise ValueError("restore baseline moved")
+    section = None
+    for path in pathlib.Path(inventory).read_text().splitlines():
+        if path in ("# staged", "# tracked", "# untracked"):
+            section = path[2:]
+            continue
+        if not section or not path or path.startswith("#"):
+            continue
+        if pathlib.PurePosixPath(path).is_absolute() or ".." in pathlib.PurePosixPath(path).parts:
+            raise ValueError("invalid inventory path")
+        file = pathlib.Path(repo, path)
+        if any(parent.is_symlink() for parent in file.parents if parent != pathlib.Path(repo) and pathlib.Path(repo) in parent.parents):
+            raise ValueError("inventory parent changed type")
+        # Unknown conflicts must never be treated as verified restoration.
+        if git("ls-files", "-u", "--", path):
+            raise ValueError("unresolved inventory path")
+        if path in skipped:
+            derived = path in ("index.md", "SCHEMA.md", "log.md") or path.endswith("/log.md") or (path.startswith("projects/") and path.count("/") == 2 and path.endswith("/knowledge.md"))
+            if not derived:
+                raise ValueError("non-derived inventory exemption")
+            want = entry(stash, path) or entry(head, path)
+        else:
+            want = entry(stash + "^3", path) if section == "untracked" else expected(path)
+        if want is None:
+            if os.path.lexists(file):
+                raise ValueError("deleted inventory path reappeared")
+            continue
+        mode, oid = want
+        if mode == "120000":
+            if not file.is_symlink():
+                raise ValueError("inventory symlink type changed")
+            data = os.fsencode(os.readlink(file))
+        else:
+            if file.is_symlink() or not file.is_file():
+                raise ValueError("inventory regular file missing or type changed")
+            if mode not in ("100644", "100755"):
+                raise ValueError("unsupported inventory mode")
+            if bool(file.stat().st_mode & 0o111) != (mode == "100755"):
+                raise ValueError("inventory executable mode changed")
+            data = None
+        if path not in skipped:
+            if data is None:
+                with file.open("rb") as stream:
+                    actual = git("hash-object", "--stdin", stream=stream)
+            else:
+                actual = git("hash-object", "--stdin", data=data)
+            if actual.decode().strip() != oid:
+                raise ValueError("inventory content mismatch")
+
+
+if __name__ == "__main__":
+    try:
+        repo, inventory, stash, head, skip = sys.argv[1:]
+        verify(repo, inventory, stash, head, set(skip.splitlines()))
+    except (OSError, ValueError, subprocess.SubprocessError):
+        print("inventory verification refused: missing, changed or ambiguous restore", file=sys.stderr)
+        sys.exit(1)

package/dist/vault-sync/scripts/wiki-pull-with-auto-resolve.sh

@@ -220,6 +220,7 @@ try_auto_resolve_derived_conflicts() {
         cmd_rc=$?
         printf '%s\n' "$resolver_out" >>"$LOG_FILE"
         if [ "$cmd_rc" -eq 0 ]; then
+            RESOLVED_PATHS="$(printf '%s\n' "$resolver_out" | python3 -c 'import json,sys; print("\n".join(json.load(sys.stdin)["data"]["resolved_paths"]))')" || return 1
             log "AUTO-RESOLVE composite derived artifacts op=$op_id"
             return 0
         elif [ "$cmd_rc" -eq 60 ]; then
@@ -243,6 +244,7 @@ except: pass
         cmd_rc=$?
         printf '%s\n' "$resolver_out" >>"$LOG_FILE"
         if [ "$cmd_rc" -eq 0 ]; then
+            RESOLVED_PATHS="$(printf '%s\n' "$resolver_out" | python3 -c 'import json,sys; print("\n".join(json.load(sys.stdin)["data"]["resolved_paths"]))')" || return 1
             log "AUTO-RESOLVE composite derived artifacts op=$op_id (skillwiki)"
             return 0
         elif [ "$cmd_rc" -eq 60 ]; then
@@ -615,12 +617,11 @@ while [ $REBASE_RC -ne 0 ]; do
         continue
     fi
 
-    if try_auto_resolve_derived_conflicts "$OP_ID"; then
-        if ! GIT_EDITOR=true git rebase --continue 2>>"$LOG_FILE"; then
-            REBASE_RC=$?
-        else
-            REBASE_RC=0
-        fi
+    RESOLVER_RC=0
+    try_auto_resolve_derived_conflicts "$OP_ID" || RESOLVER_RC=$?
+    if [ "$RESOLVER_RC" -eq 0 ]; then
+        GIT_EDITOR=true git rebase --continue 2>>"$LOG_FILE"
+        REBASE_RC=$?
         continue
     fi
 
@@ -628,8 +629,7 @@ while [ $REBASE_RC -ne 0 ]; do
     # The unknown paths must go through the manual-conflict path (retry/handoff).
     # The derived paths are already git-added; rebase --continue will fail on
     # the remaining unknowns, so we go straight to handle_manual_conflict.
-    if [ "$?" -eq 60 ]; then
-        local unknown_conflicts
+    if [ "$RESOLVER_RC" -eq 60 ]; then
         unknown_conflicts="$(git diff --name-only --diff-filter=U 2>/dev/null)"
         if [ -n "$unknown_conflicts" ]; then
             STOPPED_SHA=$(cat "$WIKI_DIR/.git/rebase-merge/stopped-sha" 2>/dev/null || echo "")
@@ -659,6 +659,7 @@ while [ $REBASE_RC -ne 0 ]; do
 done
 
 if [ -n "$OWNED_STASH_OID" ]; then
+  vault_sync_op_set_field "$WIKI_DIR" "$OP_ID" restore_head "$(git rev-parse HEAD)" || exit 1
   if vault_sync_op_stash_apply_owned "$WIKI_DIR" "$OWNED_STASH_OID" 2>>"$LOG_FILE"; then
     if ! vault_sync_op_verify_inventory "$WIKI_DIR" "$OP_ID" "$OWNED_STASH_OID" 2>>"$LOG_FILE"; then
       vault_sync_op_mark_review_required "$WIKI_DIR" "$OP_ID" "inventory-verify-failed"
@@ -673,7 +674,12 @@ if [ -n "$OWNED_STASH_OID" ]; then
   else
     CONFLICTS=$(git diff --name-only --diff-filter=U 2>/dev/null)
     vault_sync_op_set_phase "$WIKI_DIR" "$OP_ID" "restoring"
-    if [ -n "$CONFLICTS" ] && try_auto_resolve_derived_conflicts "$OP_ID"; then
+    RESOLVER_RC=1
+    if [ -n "$CONFLICTS" ]; then
+      RESOLVER_RC=0
+      try_auto_resolve_derived_conflicts "$OP_ID" || RESOLVER_RC=$?
+    fi
+    if [ "$RESOLVER_RC" -eq 0 ]; then
       if [ -n "$(git diff --name-only --diff-filter=U 2>/dev/null)" ]; then
         vault_sync_op_mark_review_required "$WIKI_DIR" "$OP_ID" "stash-restore-conflicts"
         log "FAIL stash apply derived auto-resolve left conflicts"
@@ -681,7 +687,7 @@ if [ -n "$OWNED_STASH_OID" ]; then
       fi
       # Derived regeneration rewrites conflicted paths; verify presence for those
       # paths and content for everything else.
-      SKIP_CONTENT="$(printf '%s\n' $CONFLICTS)"
+      SKIP_CONTENT="${RESOLVED_PATHS:-}"
       if ! vault_sync_op_verify_inventory "$WIKI_DIR" "$OP_ID" "$OWNED_STASH_OID" "$SKIP_CONTENT" 2>>"$LOG_FILE"; then
         vault_sync_op_mark_review_required "$WIKI_DIR" "$OP_ID" "inventory-verify-failed"
         log "FAIL inventory verification after derived auto-resolve oid=$OWNED_STASH_OID"
@@ -690,7 +696,7 @@ if [ -n "$OWNED_STASH_OID" ]; then
 
       vault_sync_op_stash_drop_owned "$WIKI_DIR" "$OWNED_STASH_OID" 2>>"$LOG_FILE" || true
       log "STASH apply derived conflicts auto-resolved"
-    elif [ -n "$CONFLICTS" ] && [ "$?" -eq 60 ]; then
+    elif [ "$RESOLVER_RC" -eq 60 ]; then
       # M4: Partial-decline during stash-apply. The resolver resolved the
       # derived subset and returned resolved_paths. Unknown paths remain
       # conflicted — surface as review-required.
@@ -704,11 +710,7 @@ if [ -n "$OWNED_STASH_OID" ]; then
       # derived paths. The conflict set alone is insufficient because the
       # resolver regenerates derived files that may not have been in the
       # stash-apply conflict set (derived-conflicts.ts:100-134).
-      SKIP_CONTENT="$(printf '%s\n' $CONFLICTS)"
-      if [ -n "${RESOLVED_PATHS:-}" ]; then
-        SKIP_CONTENT="${SKIP_CONTENT}
-${RESOLVED_PATHS}"
-      fi
+      SKIP_CONTENT="${RESOLVED_PATHS:-}"
       if ! vault_sync_op_verify_inventory "$WIKI_DIR" "$OP_ID" "$OWNED_STASH_OID" "$SKIP_CONTENT" 2>>"$LOG_FILE"; then
         vault_sync_op_mark_review_required "$WIKI_DIR" "$OP_ID" "inventory-verify-failed-partial"
         log "FAIL inventory verification after partial-decline oid=$OWNED_STASH_OID"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "skillwiki",
-  "version": "0.10.114",
+  "version": "0.10.116",
   "type": "module",
   "bin": {
     "skillwiki": "dist/cli.js",

package/skills/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "skillwiki",
-  "version": "0.10.114",
+  "version": "0.10.116",
   "skills": "./",
   "description": "Project-aware Karpathy-style knowledge base for Claude Code: 22 prompt-only skills (wiki-*, proj-*, using-skillwiki, skillwiki-mcp, skillwiki-connect) backed by the deterministic `skillwiki` CLI.",
   "author": {

package/skills/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "skillwiki",
-  "version": "0.10.114",
+  "version": "0.10.116",
   "description": "Project-aware Karpathy-style knowledge base for Codex with 22 prompt-only skills backed by the deterministic skillwiki CLI.",
   "author": {
     "name": "karlorz",

package/skills/.cursor-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "skillwiki",
-  "version": "0.10.114",
+  "version": "0.10.116",
   "description": "Project-aware Karpathy-style knowledge base: 22 prompt-only skills (wiki-*, proj-*, using-skillwiki, skillwiki-mcp, skillwiki-connect) backed by HTTP MCP wiki_capture.",
   "author": {
     "name": "karlorz"

package/skills/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@skillwiki/skills",
-  "version": "0.10.114",
+  "version": "0.10.116",
   "private": true,
   "files": [
     "wiki-*",

package/dist/{chunk-XJ5VEIH7.js → chunk-4ZKCGX4V.js}

@@ -1,7 +1,4 @@
 #!/usr/bin/env node
-import {
-  atomicWriteText
-} from "./chunk-6VUK2FTX.js";
 import {
   PRODUCTION_MIRROR_LABEL,
   PRODUCTION_WATCHER_LABEL,
@@ -15,6 +12,9 @@ import {
 import {
   parseDotenvFile
 } from "./chunk-IJKJGQKL.js";
+import {
+  atomicWriteText
+} from "./chunk-6VUK2FTX.js";
 
 // src/clip-outbox/migrate.ts
 import { access, mkdir, readFile } from "fs/promises";

package/dist/{chunk-FQERKMD7.js → chunk-CNELLIZ2.js}

@@ -35,15 +35,15 @@ import {
   splitFrontmatter,
   vaultIoConcurrency
 } from "./chunk-JL2SCLXT.js";
-import {
-  atomicWriteText
-} from "./chunk-6VUK2FTX.js";
 import {
   parseDotenvFile,
   parseDotenvText,
   profileKey,
   resolveSkillwikiHome
 } from "./chunk-IJKJGQKL.js";
+import {
+  atomicWriteText
+} from "./chunk-6VUK2FTX.js";
 import {
   ExitCode,
   FleetManifestSchema,

package/dist/{watcher-VJ3TOU6J.js → watcher-2PBZQLKL.js}

@@ -1,9 +1,4 @@
 #!/usr/bin/env node
-import {
-  readJournal,
-  upsertJournal,
-  writeJournal
-} from "./chunk-SEY4N4CT.js";
 import {
   buildReadyHint
 } from "./chunk-OSL4J7GF.js";
@@ -14,10 +9,15 @@ import {
   sha256Hex
 } from "./chunk-ZRGZBAVS.js";
 import "./chunk-QESNTTVY.js";
-import "./chunk-6VUK2FTX.js";
 import {
   assertPublicHttpsUrl
 } from "./chunk-5D5HFQ76.js";
+import {
+  readJournal,
+  upsertJournal,
+  writeJournal
+} from "./chunk-SEY4N4CT.js";
+import "./chunk-6VUK2FTX.js";
 import "./chunk-VNSZCK5V.js";
 
 // src/clip-outbox/watcher.ts