akm-cli 0.9.0-beta.2 → 0.9.0-beta.26

package/dist/scripts/migrate-storage.js

@@ -491,349 +491,6 @@ var init_env = __esm(() => {
   ASSIGN_RE = /^\s*(?:export\s+)?([A-Za-z_][A-Za-z0-9_]*)\s*=/;
 });
 
-// src/core/asset/frontmatter.ts
-function parseFrontmatter(raw) {
-  const parsedBlock = parseFrontmatterBlock(raw);
-  if (!parsedBlock) {
-    return { data: {}, content: raw, frontmatter: null, bodyStartLine: 1 };
-  }
-  const data = {};
-  let currentKey = null;
-  let mode = "scalar";
-  let nested = null;
-  let currentList = null;
-  let blockLines = null;
-  let blockChomping = "clip";
-  const flushPending = () => {
-    if (mode === "pending" && currentKey !== null) {
-      data[currentKey] = "";
-    }
-  };
-  const flushBlock = () => {
-    if (mode !== "block" || currentKey === null || blockLines === null)
-      return;
-    const deindented = blockLines.map((l) => l.startsWith("  ") ? l.slice(2) : l);
-    if (blockChomping === "keep") {
-      data[currentKey] = deindented.join(`
-`);
-    } else if (blockChomping === "strip") {
-      data[currentKey] = deindented.join(`
-`).replace(/\n+$/, "");
-    } else {
-      data[currentKey] = `${deindented.join(`
-`).replace(/\n+$/, "")}
-`;
-    }
-  };
-  for (const line of parsedBlock.frontmatter.split(/\r?\n/)) {
-    if (mode === "block") {
-      if (line.startsWith("  ") || line === "") {
-        blockLines.push(line);
-        continue;
-      }
-      flushBlock();
-      mode = "scalar";
-      blockLines = null;
-    }
-    const seqItem = line.match(/^(?: {2})?- (.*)$/);
-    if (seqItem && currentKey !== null && (mode === "list" || mode === "pending")) {
-      if (mode === "pending") {
-        currentList = [];
-        data[currentKey] = currentList;
-        mode = "list";
-      }
-      currentList.push(parseYamlScalar(seqItem[1].trim()));
-      continue;
-    }
-    if (mode === "scalar" && currentKey !== null && /^ {2}\S/.test(line)) {
-      data[currentKey] = `${String(data[currentKey])} ${line.trim()}`;
-      continue;
-    }
-    const indented = line.match(/^ {2}(\w[\w-]*):\s*(.+)$/);
-    if (indented && currentKey !== null && (mode === "object" || mode === "pending")) {
-      if (mode === "pending") {
-        nested = {};
-        data[currentKey] = nested;
-        mode = "object";
-      }
-      nested[indented[1]] = parseYamlScalar(indented[2].trim());
-      continue;
-    }
-    const top = line.match(/^(\w[\w-]*):\s*(.*)$/);
-    if (!top) {
-      continue;
-    }
-    flushPending();
-    currentKey = top[1];
-    const value = top[2].trim();
-    if (value === "|" || value === "|-" || value === "|+") {
-      mode = "block";
-      blockLines = [];
-      blockChomping = value === "|-" ? "strip" : value === "|+" ? "keep" : "clip";
-      nested = null;
-      currentList = null;
-    } else if (value === "") {
-      mode = "pending";
-      nested = null;
-      currentList = null;
-    } else if (value.startsWith("[") && value.endsWith("]")) {
-      mode = "list";
-      nested = null;
-      currentList = null;
-      currentList = parseFlowArray(value);
-      data[currentKey] = currentList;
-    } else {
-      mode = "scalar";
-      nested = null;
-      currentList = null;
-      data[currentKey] = parseYamlScalar(value);
-    }
-  }
-  if (mode === "block") {
-    flushBlock();
-  }
-  flushPending();
-  return {
-    data,
-    content: parsedBlock.content,
-    frontmatter: parsedBlock.frontmatter,
-    bodyStartLine: parsedBlock.bodyStartLine
-  };
-}
-function parseFlowArray(value) {
-  const inner = value.slice(1, -1).trim();
-  if (!inner)
-    return [];
-  return inner.split(",").map((item) => parseYamlScalar(item.trim()));
-}
-function parseFrontmatterBlock(raw) {
-  const match = raw.match(/^---\r?\n([\s\S]*?)\r?\n---(?:\r\n|\r|\n|$)([\s\S]*)$/);
-  if (!match)
-    return null;
-  const frontmatter = match[1].replace(/\r/g, "");
-  const content = match[2];
-  return {
-    frontmatter,
-    content,
-    bodyStartLine: countLines(raw.slice(0, match[0].length - match[2].length)) + 1
-  };
-}
-function countLines(text) {
-  if (text.length === 0)
-    return 0;
-  return text.split(/\r?\n/).length - 1;
-}
-function parseYamlScalar(value) {
-  if (value === "")
-    return "";
-  if (value === "true")
-    return true;
-  if (value === "false")
-    return false;
-  const asNumber = Number(value);
-  if (!Number.isNaN(asNumber))
-    return asNumber;
-  if (value.startsWith('"') && value.endsWith('"') || value.startsWith("'") && value.endsWith("'")) {
-    return value.slice(1, -1);
-  }
-  return value;
-}
-
-// src/core/asset/markdown.ts
-function parseMarkdownToc(content) {
-  const lines = content.split(/\r?\n/);
-  const headings = [];
-  const parsed = parseFrontmatter(content);
-  const start = parsed.frontmatter ? parsed.bodyStartLine - 1 : 0;
-  for (let i = start;i < lines.length; i++) {
-    const match = lines[i].match(/^(#{1,6})\s+(.+)$/);
-    if (match) {
-      headings.push({
-        level: match[1].length,
-        text: match[2].replace(/\s+#+\s*$/, "").trim(),
-        line: i + 1
-      });
-    }
-  }
-  return { headings, totalLines: lines.length };
-}
-var init_markdown = () => {};
-
-// src/core/warn.ts
-import fs2 from "fs";
-function isVerbose() {
-  const env = process.env.AKM_VERBOSE?.trim().toLowerCase();
-  if (env === "1" || env === "true" || env === "yes" || env === "on")
-    return true;
-  if (env === "0" || env === "false" || env === "no" || env === "off")
-    return false;
-  return verbose;
-}
-function appendToLogFile(level, args) {
-  if (!logFilePath)
-    return;
-  const ts = new Date().toISOString();
-  const msg = args.map((a) => typeof a === "string" ? a : JSON.stringify(a)).join(" ");
-  try {
-    fs2.appendFileSync(logFilePath, `[${ts}] [${level}] ${msg}
-`);
-  } catch (e) {
-    process.stderr.write(`[akm:warn] log-file write failed (${logFilePath}): ${e}
-`);
-    process.stderr.write(`[${ts}] [${level}] ${msg}
-`);
-  }
-}
-function warn(...args) {
-  appendToLogFile("WARN", args);
-  if (!quiet) {
-    console.warn(...args);
-  }
-}
-function error(...args) {
-  appendToLogFile("ERROR", args);
-  if (!quiet) {
-    console.error(...args);
-  }
-}
-function warnVerbose(...args) {
-  if (isVerbose()) {
-    warn(...args);
-  }
-}
-var quiet = false, verbose = false, logFilePath;
-var init_warn = () => {};
-
-// src/indexer/walk/file-context.ts
-var renderers;
-var init_file_context = __esm(() => {
-  init_common();
-  renderers = new Map;
-});
-
-// src/indexer/passes/metadata-contributors.ts
-function registerMetadataContributor(contributor) {
-  contributors.push(contributor);
-}
-var contributors;
-var init_metadata_contributors = __esm(() => {
-  contributors = [];
-});
-
-// src/indexer/passes/metadata.ts
-import fs3 from "fs";
-function extractDescriptionFromComments(filePath) {
-  let content;
-  try {
-    content = fs3.readFileSync(filePath, "utf8");
-  } catch {
-    return null;
-  }
-  const lines = content.split(/\r?\n/).slice(0, 50);
-  const blockStart = lines.findIndex((l) => /^\s*\/\*\*/.test(l));
-  if (blockStart >= 0) {
-    const desc = [];
-    for (let i = blockStart;i < lines.length; i++) {
-      const line = lines[i];
-      if (i > blockStart && /\*\//.test(line))
-        break;
-      const cleaned = line.replace(/^\s*\/?\*\*?\s?/, "").replace(/\*\/\s*$/, "").trim();
-      if (cleaned)
-        desc.push(cleaned);
-    }
-    if (desc.length > 0)
-      return desc.join(" ");
-  }
-  let start = 0;
-  if (lines[0]?.startsWith("#!"))
-    start = 1;
-  const hashLines = [];
-  for (let i = start;i < lines.length; i++) {
-    const line = lines[i].trim();
-    if (line.startsWith("#") && !line.startsWith("#!")) {
-      hashLines.push(line.replace(/^#+\s*/, "").trim());
-    } else if (line === "") {} else {
-      break;
-    }
-  }
-  if (hashLines.length > 0)
-    return hashLines.join(" ");
-  return null;
-}
-var KNOWN_QUALITY_VALUES, warnedUnknownQualityValues, WIKI_INFRA_FILES;
-var init_metadata = __esm(() => {
-  init_asset_spec();
-  init_common();
-  init_warn();
-  init_file_context();
-  init_metadata_contributors();
-  KNOWN_QUALITY_VALUES = new Set(["generated", "curated", "enriched", "proposed"]);
-  warnedUnknownQualityValues = new Set;
-  WIKI_INFRA_FILES = new Set(["schema.md", "index.md", "log.md"]);
-});
-
-// src/core/asset/asset-ref.ts
-import path from "path";
-function parseAssetRef(ref) {
-  const trimmed = ref.trim();
-  if (!trimmed)
-    throw new UsageError("Empty ref.", "MISSING_REQUIRED_ARGUMENT");
-  let origin;
-  let body = trimmed;
-  const boundary = trimmed.indexOf("//");
-  if (boundary >= 0) {
-    origin = trimmed.slice(0, boundary);
-    body = trimmed.slice(boundary + 2);
-    if (!origin)
-      throw new UsageError("Empty origin in ref.", "MISSING_REQUIRED_ARGUMENT");
-  }
-  const colon = body.indexOf(":");
-  if (colon <= 0) {
-    throw new UsageError(`Invalid ref "${trimmed}". Expected [origin//]type:name, e.g. skill:deploy or knowledge:guide.md`, "MISSING_REQUIRED_ARGUMENT");
-  }
-  const rawType = body.slice(0, colon);
-  const rawName = body.slice(colon + 1);
-  if (rawType === "vault") {
-    throw new UsageError("The `vault` asset type was removed in 0.9.0 \u2014 use `env:` (whole .env config) or `secret:` (a single value).", "MISSING_REQUIRED_ARGUMENT");
-  }
-  const resolvedType = TYPE_ALIASES[rawType] ?? rawType;
-  if (!isAssetType(resolvedType)) {
-    throw new UsageError(`Invalid asset type: "${rawType}".`, "MISSING_REQUIRED_ARGUMENT");
-  }
-  validateName(rawName);
-  const name = normalizeName(rawName);
-  return { type: resolvedType, name, origin: origin || undefined };
-}
-function validateName(name) {
-  if (!name)
-    throw new UsageError("Empty asset name.", "MISSING_REQUIRED_ARGUMENT");
-  if (name.includes("\x00"))
-    throw new UsageError("Null byte in asset name.", "MISSING_REQUIRED_ARGUMENT");
-  if (/^[A-Za-z]:/.test(name))
-    throw new UsageError("Windows drive path in asset name.", "MISSING_REQUIRED_ARGUMENT");
-  const normalized = path.posix.normalize(name.replace(/\\/g, "/"));
-  if (path.posix.isAbsolute(normalized))
-    throw new UsageError("Absolute path in asset name.", "MISSING_REQUIRED_ARGUMENT");
-  if (normalized === ".." || normalized.startsWith("../")) {
-    throw new UsageError("Path traversal in asset name.", "MISSING_REQUIRED_ARGUMENT");
-  }
-  const segments = normalized.split("/");
-  if (segments.some((seg) => seg === "." || seg === "..")) {
-    throw new UsageError("Asset name cannot contain relative path segments.", "MISSING_REQUIRED_ARGUMENT");
-  }
-}
-function normalizeName(name) {
-  return path.posix.normalize(name.replace(/\\/g, "/"));
-}
-var TYPE_ALIASES;
-var init_asset_ref = __esm(() => {
-  init_common();
-  init_errors();
-  TYPE_ALIASES = {
-    environment: "env"
-  };
-});
-
 // node_modules/yaml/dist/nodes/identity.js
 var require_identity = __commonJS((exports) => {
   var ALIAS = Symbol.for("yaml.alias");
@@ -906,17 +563,17 @@ var require_visit = __commonJS((exports) => {
   visit.BREAK = BREAK;
   visit.SKIP = SKIP;
   visit.REMOVE = REMOVE;
-  function visit_(key, node, visitor, path2) {
-    const ctrl = callVisitor(key, node, visitor, path2);
+  function visit_(key, node, visitor, path) {
+    const ctrl = callVisitor(key, node, visitor, path);
     if (identity.isNode(ctrl) || identity.isPair(ctrl)) {
-      replaceNode(key, path2, ctrl);
-      return visit_(key, ctrl, visitor, path2);
+      replaceNode(key, path, ctrl);
+      return visit_(key, ctrl, visitor, path);
     }
     if (typeof ctrl !== "symbol") {
       if (identity.isCollection(node)) {
-        path2 = Object.freeze(path2.concat(node));
+        path = Object.freeze(path.concat(node));
         for (let i = 0;i < node.items.length; ++i) {
-          const ci = visit_(i, node.items[i], visitor, path2);
+          const ci = visit_(i, node.items[i], visitor, path);
           if (typeof ci === "number")
             i = ci - 1;
           else if (ci === BREAK)
@@ -927,13 +584,13 @@ var require_visit = __commonJS((exports) => {
           }
         }
       } else if (identity.isPair(node)) {
-        path2 = Object.freeze(path2.concat(node));
-        const ck = visit_("key", node.key, visitor, path2);
+        path = Object.freeze(path.concat(node));
+        const ck = visit_("key", node.key, visitor, path);
         if (ck === BREAK)
           return BREAK;
         else if (ck === REMOVE)
           node.key = null;
-        const cv = visit_("value", node.value, visitor, path2);
+        const cv = visit_("value", node.value, visitor, path);
         if (cv === BREAK)
           return BREAK;
         else if (cv === REMOVE)
@@ -954,17 +611,17 @@ var require_visit = __commonJS((exports) => {
   visitAsync.BREAK = BREAK;
   visitAsync.SKIP = SKIP;
   visitAsync.REMOVE = REMOVE;
-  async function visitAsync_(key, node, visitor, path2) {
-    const ctrl = await callVisitor(key, node, visitor, path2);
+  async function visitAsync_(key, node, visitor, path) {
+    const ctrl = await callVisitor(key, node, visitor, path);
     if (identity.isNode(ctrl) || identity.isPair(ctrl)) {
-      replaceNode(key, path2, ctrl);
-      return visitAsync_(key, ctrl, visitor, path2);
+      replaceNode(key, path, ctrl);
+      return visitAsync_(key, ctrl, visitor, path);
     }
     if (typeof ctrl !== "symbol") {
       if (identity.isCollection(node)) {
-        path2 = Object.freeze(path2.concat(node));
+        path = Object.freeze(path.concat(node));
         for (let i = 0;i < node.items.length; ++i) {
-          const ci = await visitAsync_(i, node.items[i], visitor, path2);
+          const ci = await visitAsync_(i, node.items[i], visitor, path);
           if (typeof ci === "number")
             i = ci - 1;
           else if (ci === BREAK)
@@ -975,13 +632,13 @@ var require_visit = __commonJS((exports) => {
           }
         }
       } else if (identity.isPair(node)) {
-        path2 = Object.freeze(path2.concat(node));
-        const ck = await visitAsync_("key", node.key, visitor, path2);
+        path = Object.freeze(path.concat(node));
+        const ck = await visitAsync_("key", node.key, visitor, path);
         if (ck === BREAK)
           return BREAK;
         else if (ck === REMOVE)
           node.key = null;
-        const cv = await visitAsync_("value", node.value, visitor, path2);
+        const cv = await visitAsync_("value", node.value, visitor, path);
         if (cv === BREAK)
           return BREAK;
         else if (cv === REMOVE)
@@ -1008,23 +665,23 @@ var require_visit = __commonJS((exports) => {
     }
     return visitor;
   }
-  function callVisitor(key, node, visitor, path2) {
+  function callVisitor(key, node, visitor, path) {
     if (typeof visitor === "function")
-      return visitor(key, node, path2);
+      return visitor(key, node, path);
     if (identity.isMap(node))
-      return visitor.Map?.(key, node, path2);
+      return visitor.Map?.(key, node, path);
     if (identity.isSeq(node))
-      return visitor.Seq?.(key, node, path2);
+      return visitor.Seq?.(key, node, path);
     if (identity.isPair(node))
-      return visitor.Pair?.(key, node, path2);
+      return visitor.Pair?.(key, node, path);
     if (identity.isScalar(node))
-      return visitor.Scalar?.(key, node, path2);
+      return visitor.Scalar?.(key, node, path);
     if (identity.isAlias(node))
-      return visitor.Alias?.(key, node, path2);
+      return visitor.Alias?.(key, node, path);
     return;
   }
-  function replaceNode(key, path2, node) {
-    const parent = path2[path2.length - 1];
+  function replaceNode(key, path, node) {
+    const parent = path[path.length - 1];
     if (identity.isCollection(parent)) {
       parent.items[key] = node;
     } else if (identity.isPair(parent)) {
@@ -1150,8 +807,8 @@ var require_directives = __commonJS((exports) => {
       if (prefix) {
         try {
           return prefix + decodeURIComponent(suffix);
-        } catch (error2) {
-          onError(String(error2));
+        } catch (error) {
+          onError(String(error));
           return null;
         }
       }
@@ -1242,9 +899,9 @@ var require_anchors = __commonJS((exports) => {
           if (typeof ref === "object" && ref.anchor && (identity.isScalar(ref.node) || identity.isCollection(ref.node))) {
             ref.node.anchor = ref.anchor;
           } else {
-            const error2 = new Error("Failed to resolve repeated object (this should not happen)");
-            error2.source = source;
-            throw error2;
+            const error = new Error("Failed to resolve repeated object (this should not happen)");
+            error.source = source;
+            throw error;
           }
         }
       },
@@ -1583,10 +1240,10 @@ var require_Collection = __commonJS((exports) => {
   var createNode = require_createNode();
   var identity = require_identity();
   var Node = require_Node();
-  function collectionFromPath(schema, path2, value) {
+  function collectionFromPath(schema, path, value) {
     let v = value;
-    for (let i = path2.length - 1;i >= 0; --i) {
-      const k = path2[i];
+    for (let i = path.length - 1;i >= 0; --i) {
+      const k = path[i];
       if (typeof k === "number" && Number.isInteger(k) && k >= 0) {
         const a = [];
         a[k] = v;
@@ -1605,7 +1262,7 @@ var require_Collection = __commonJS((exports) => {
       sourceObjects: new Map
     });
   }
-  var isEmptyPath = (path2) => path2 == null || typeof path2 === "object" && !!path2[Symbol.iterator]().next().done;
+  var isEmptyPath = (path) => path == null || typeof path === "object" && !!path[Symbol.iterator]().next().done;
 
   class Collection extends Node.NodeBase {
     constructor(type, schema) {
@@ -1626,11 +1283,11 @@ var require_Collection = __commonJS((exports) => {
         copy.range = this.range.slice();
       return copy;
     }
-    addIn(path2, value) {
-      if (isEmptyPath(path2))
+    addIn(path, value) {
+      if (isEmptyPath(path))
         this.add(value);
       else {
-        const [key, ...rest] = path2;
+        const [key, ...rest] = path;
         const node = this.get(key, true);
         if (identity.isCollection(node))
           node.addIn(rest, value);
@@ -1640,8 +1297,8 @@ var require_Collection = __commonJS((exports) => {
           throw new Error(`Expected YAML collection at ${key}. Remaining path: ${rest}`);
       }
     }
-    deleteIn(path2) {
-      const [key, ...rest] = path2;
+    deleteIn(path) {
+      const [key, ...rest] = path;
       if (rest.length === 0)
         return this.delete(key);
       const node = this.get(key, true);
@@ -1650,8 +1307,8 @@ var require_Collection = __commonJS((exports) => {
       else
         throw new Error(`Expected YAML collection at ${key}. Remaining path: ${rest}`);
     }
-    getIn(path2, keepScalar) {
-      const [key, ...rest] = path2;
+    getIn(path, keepScalar) {
+      const [key, ...rest] = path;
       const node = this.get(key, true);
       if (rest.length === 0)
         return !keepScalar && identity.isScalar(node) ? node.value : node;
@@ -1666,15 +1323,15 @@ var require_Collection = __commonJS((exports) => {
         return n == null || allowScalar && identity.isScalar(n) && n.value == null && !n.commentBefore && !n.comment && !n.tag;
       });
     }
-    hasIn(path2) {
-      const [key, ...rest] = path2;
+    hasIn(path) {
+      const [key, ...rest] = path;
       if (rest.length === 0)
         return this.has(key);
       const node = this.get(key, true);
       return identity.isCollection(node) ? node.hasIn(rest) : false;
     }
-    setIn(path2, value) {
-      const [key, ...rest] = path2;
+    setIn(path, value) {
+      const [key, ...rest] = path;
       if (rest.length === 0) {
         this.set(key, value);
       } else {
@@ -2409,7 +2066,7 @@ var require_log = __commonJS((exports) => {
     if (logLevel === "debug")
       console.log(...messages);
   }
-  function warn2(logLevel, warning) {
+  function warn(logLevel, warning) {
     if (logLevel === "debug" || logLevel === "warn") {
       if (typeof node_process.emitWarning === "function")
         node_process.emitWarning(warning);
@@ -2418,7 +2075,7 @@ var require_log = __commonJS((exports) => {
     }
   }
   exports.debug = debug;
-  exports.warn = warn2;
+  exports.warn = warn;
 });
 
 // node_modules/yaml/dist/schema/yaml-1.1/merge.js
@@ -4067,9 +3724,9 @@ var require_Document = __commonJS((exports) => {
       if (assertCollection(this.contents))
         this.contents.add(value);
     }
-    addIn(path2, value) {
+    addIn(path, value) {
       if (assertCollection(this.contents))
-        this.contents.addIn(path2, value);
+        this.contents.addIn(path, value);
     }
     createAlias(node, name) {
       if (!node.anchor) {
@@ -4118,30 +3775,30 @@ var require_Document = __commonJS((exports) => {
     delete(key) {
       return assertCollection(this.contents) ? this.contents.delete(key) : false;
     }
-    deleteIn(path2) {
-      if (Collection.isEmptyPath(path2)) {
+    deleteIn(path) {
+      if (Collection.isEmptyPath(path)) {
         if (this.contents == null)
           return false;
         this.contents = null;
         return true;
       }
-      return assertCollection(this.contents) ? this.contents.deleteIn(path2) : false;
+      return assertCollection(this.contents) ? this.contents.deleteIn(path) : false;
     }
     get(key, keepScalar) {
       return identity.isCollection(this.contents) ? this.contents.get(key, keepScalar) : undefined;
     }
-    getIn(path2, keepScalar) {
-      if (Collection.isEmptyPath(path2))
+    getIn(path, keepScalar) {
+      if (Collection.isEmptyPath(path))
         return !keepScalar && identity.isScalar(this.contents) ? this.contents.value : this.contents;
-      return identity.isCollection(this.contents) ? this.contents.getIn(path2, keepScalar) : undefined;
+      return identity.isCollection(this.contents) ? this.contents.getIn(path, keepScalar) : undefined;
     }
     has(key) {
       return identity.isCollection(this.contents) ? this.contents.has(key) : false;
     }
-    hasIn(path2) {
-      if (Collection.isEmptyPath(path2))
+    hasIn(path) {
+      if (Collection.isEmptyPath(path))
         return this.contents !== undefined;
-      return identity.isCollection(this.contents) ? this.contents.hasIn(path2) : false;
+      return identity.isCollection(this.contents) ? this.contents.hasIn(path) : false;
     }
     set(key, value) {
       if (this.contents == null) {
@@ -4150,13 +3807,13 @@ var require_Document = __commonJS((exports) => {
         this.contents.set(key, value);
       }
     }
-    setIn(path2, value) {
-      if (Collection.isEmptyPath(path2)) {
+    setIn(path, value) {
+      if (Collection.isEmptyPath(path)) {
         this.contents = value;
       } else if (this.contents == null) {
-        this.contents = Collection.collectionFromPath(this.schema, Array.from(path2), value);
+        this.contents = Collection.collectionFromPath(this.schema, Array.from(path), value);
       } else if (assertCollection(this.contents)) {
-        this.contents.setIn(path2, value);
+        this.contents.setIn(path, value);
       }
     }
     setSchema(version, options = {}) {
@@ -4255,12 +3912,12 @@ var require_errors = __commonJS((exports) => {
       super("YAMLWarning", pos, code, message);
     }
   }
-  var prettifyError = (src, lc) => (error2) => {
-    if (error2.pos[0] === -1)
+  var prettifyError = (src, lc) => (error) => {
+    if (error.pos[0] === -1)
       return;
-    error2.linePos = error2.pos.map((pos) => lc.linePos(pos));
-    const { line, col } = error2.linePos[0];
-    error2.message += ` at line ${line}, column ${col}`;
+    error.linePos = error.pos.map((pos) => lc.linePos(pos));
+    const { line, col } = error.linePos[0];
+    error.message += ` at line ${line}, column ${col}`;
     let ci = col - 1;
     let lineStr = src.substring(lc.lineStarts[line - 1], lc.lineStarts[line]).replace(/[\n\r]+$/, "");
     if (ci >= 60 && lineStr.length > 80) {
@@ -4279,12 +3936,12 @@ var require_errors = __commonJS((exports) => {
     }
     if (/[^ ]/.test(lineStr)) {
       let count = 1;
-      const end = error2.linePos[1];
+      const end = error.linePos[1];
       if (end?.line === line && end.col > col) {
         count = Math.max(1, Math.min(end.col - col, 80 - ci));
       }
       const pointer = " ".repeat(ci) + "^".repeat(count);
-      error2.message += `:
+      error.message += `:
 
 ${lineStr}
 ${pointer}
@@ -5074,7 +4731,7 @@ var require_resolve_block_scalar = __commonJS((exports) => {
     const mode = source[0];
     let indent = 0;
     let chomp = "";
-    let error2 = -1;
+    let error = -1;
     for (let i = 1;i < source.length; ++i) {
       const ch = source[i];
       if (!chomp && (ch === "-" || ch === "+"))
@@ -5083,12 +4740,12 @@ var require_resolve_block_scalar = __commonJS((exports) => {
         const n = Number(ch);
         if (!indent && n)
           indent = n;
-        else if (error2 === -1)
-          error2 = offset + i;
+        else if (error === -1)
+          error = offset + i;
       }
     }
-    if (error2 !== -1)
-      onError(error2, "UNEXPECTED_TOKEN", `Block scalar header includes extra characters: ${source}`);
+    if (error !== -1)
+      onError(error, "UNEXPECTED_TOKEN", `Block scalar header includes extra characters: ${source}`);
     let hasSpace = false;
     let comment = "";
     let length = source.length;
@@ -5375,8 +5032,8 @@ var require_compose_scalar = __commonJS((exports) => {
     try {
       const res = tag.resolve(value, (msg) => onError(tagToken ?? token, "TAG_RESOLVE_FAILED", msg), ctx.options);
       scalar = identity.isScalar(res) ? res : new Scalar.Scalar(res);
-    } catch (error2) {
-      const msg = error2 instanceof Error ? error2.message : String(error2);
+    } catch (error) {
+      const msg = error instanceof Error ? error.message : String(error);
       onError(tagToken ?? token, "TAG_RESOLVE_FAILED", msg);
       scalar = new Scalar.Scalar(value);
     }
@@ -5493,8 +5150,8 @@ var require_compose_node = __commonJS((exports) => {
           node = composeCollection.composeCollection(CN, ctx, token, props, onError);
           if (anchor)
             node.anchor = anchor.source.substring(1);
-        } catch (error2) {
-          const message = error2 instanceof Error ? error2.message : String(error2);
+        } catch (error) {
+          const message = error instanceof Error ? error.message : String(error);
           onError(token, "RESOURCE_EXHAUSTION", message);
         }
         break;
@@ -5743,11 +5400,11 @@ ${cb}` : comment;
           break;
         case "error": {
           const msg = token.source ? `${token.message}: ${JSON.stringify(token.source)}` : token.message;
-          const error2 = new errors.YAMLParseError(getErrorPos(token), "UNEXPECTED_TOKEN", msg);
+          const error = new errors.YAMLParseError(getErrorPos(token), "UNEXPECTED_TOKEN", msg);
           if (this.atDirectives || !this.doc)
-            this.errors.push(error2);
+            this.errors.push(error);
           else
-            this.doc.errors.push(error2);
+            this.doc.errors.push(error);
           break;
         }
         case "doc-end": {
@@ -6051,9 +5708,9 @@ var require_cst_visit = __commonJS((exports) => {
   visit.BREAK = BREAK;
   visit.SKIP = SKIP;
   visit.REMOVE = REMOVE;
-  visit.itemAtPath = (cst, path2) => {
+  visit.itemAtPath = (cst, path) => {
     let item = cst;
-    for (const [field, index] of path2) {
+    for (const [field, index] of path) {
       const tok = item?.[field];
       if (tok && "items" in tok) {
         item = tok.items[index];
@@ -6062,23 +5719,23 @@ var require_cst_visit = __commonJS((exports) => {
     }
     return item;
   };
-  visit.parentCollection = (cst, path2) => {
-    const parent = visit.itemAtPath(cst, path2.slice(0, -1));
-    const field = path2[path2.length - 1][0];
+  visit.parentCollection = (cst, path) => {
+    const parent = visit.itemAtPath(cst, path.slice(0, -1));
+    const field = path[path.length - 1][0];
     const coll = parent?.[field];
     if (coll && "items" in coll)
       return coll;
     throw new Error("Parent collection not found");
   };
-  function _visit(path2, item, visitor) {
-    let ctrl = visitor(item, path2);
+  function _visit(path, item, visitor) {
+    let ctrl = visitor(item, path);
     if (typeof ctrl === "symbol")
       return ctrl;
     for (const field of ["key", "value"]) {
       const token = item[field];
       if (token && "items" in token) {
         for (let i = 0;i < token.items.length; ++i) {
-          const ci = _visit(Object.freeze(path2.concat([[field, i]])), token.items[i], visitor);
+          const ci = _visit(Object.freeze(path.concat([[field, i]])), token.items[i], visitor);
           if (typeof ci === "number")
             i = ci - 1;
           else if (ci === BREAK)
@@ -6089,10 +5746,10 @@ var require_cst_visit = __commonJS((exports) => {
           }
         }
         if (typeof ctrl === "function" && field === "key")
-          ctrl = ctrl(item, path2);
+          ctrl = ctrl(item, path);
       }
     }
-    return typeof ctrl === "function" ? ctrl(item, path2) : ctrl;
+    return typeof ctrl === "function" ? ctrl(item, path) : ctrl;
   }
   exports.visit = visit;
 });
@@ -7020,8 +6677,8 @@ var require_parser = __commonJS((exports) => {
     peek(n) {
       return this.stack[this.stack.length - n];
     }
-    *pop(error2) {
-      const token = error2 ?? this.stack.pop();
+    *pop(error) {
+      const token = error ?? this.stack.pop();
       if (!token) {
         const message = "Tried to pop an empty stack";
         yield { type: "error", offset: this.offset, source: "", message };
@@ -7361,14 +7018,14 @@ var require_parser = __commonJS((exports) => {
           case "scalar":
           case "single-quoted-scalar":
           case "double-quoted-scalar": {
-            const fs4 = this.flowScalar(this.type);
+            const fs2 = this.flowScalar(this.type);
             if (atNextItem || it.value) {
-              map.items.push({ start, key: fs4, sep: [] });
+              map.items.push({ start, key: fs2, sep: [] });
               this.onKeyLine = true;
             } else if (it.sep) {
-              this.stack.push(fs4);
+              this.stack.push(fs2);
             } else {
-              Object.assign(it, { key: fs4, sep: [] });
+              Object.assign(it, { key: fs2, sep: [] });
               this.onKeyLine = true;
             }
             return;
@@ -7496,13 +7153,13 @@ var require_parser = __commonJS((exports) => {
           case "scalar":
           case "single-quoted-scalar":
           case "double-quoted-scalar": {
-            const fs4 = this.flowScalar(this.type);
+            const fs2 = this.flowScalar(this.type);
             if (!it || it.value)
-              fc.items.push({ start: [], key: fs4, sep: [] });
+              fc.items.push({ start: [], key: fs2, sep: [] });
             else if (it.sep)
-              this.stack.push(fs4);
+              this.stack.push(fs2);
             else
-              Object.assign(it, { key: fs4, sep: [] });
+              Object.assign(it, { key: fs2, sep: [] });
             return;
           }
           case "flow-map-end":
@@ -7804,7 +7461,301 @@ var init_dist = __esm(() => {
   $visitAsync = visit.visitAsync;
 });
 
-// src/workflows/schema.ts
+// src/core/asset/frontmatter.ts
+function parseFrontmatter(raw) {
+  const parsedBlock = parseFrontmatterBlock(raw);
+  if (!parsedBlock) {
+    return { data: {}, content: raw, frontmatter: null, bodyStartLine: 1 };
+  }
+  let data = {};
+  if (parsedBlock.frontmatter.trim()) {
+    try {
+      const parsed = $parse(parsedBlock.frontmatter);
+      if (parsed !== null && typeof parsed === "object" && !Array.isArray(parsed)) {
+        data = normalizeYamlValues(parsed);
+      }
+    } catch {
+      data = parseFrontmatterLenient(parsedBlock.frontmatter);
+    }
+  }
+  return {
+    data,
+    content: parsedBlock.content,
+    frontmatter: parsedBlock.frontmatter,
+    bodyStartLine: parsedBlock.bodyStartLine
+  };
+}
+function normalizeYamlValues(value) {
+  if (value instanceof Date) {
+    const y = value.getUTCFullYear();
+    const m = String(value.getUTCMonth() + 1).padStart(2, "0");
+    const d = String(value.getUTCDate()).padStart(2, "0");
+    return `${y}-${m}-${d}`;
+  }
+  if (value === null)
+    return "";
+  if (Array.isArray(value))
+    return value.map(normalizeYamlValues);
+  if (typeof value === "object") {
+    return Object.fromEntries(Object.entries(value).map(([k, v]) => [k, normalizeYamlValues(v)]));
+  }
+  return value;
+}
+function parseFrontmatterLenient(frontmatter) {
+  const data = {};
+  for (const line of frontmatter.split(/\r?\n/)) {
+    const m = line.match(/^([\w][\w-]*):\s*(.*)$/);
+    if (!m)
+      continue;
+    const key = m[1];
+    const rawValue = (m[2] ?? "").trim();
+    try {
+      const singleEntry = $parse(`k: ${rawValue}`);
+      if (singleEntry !== null && typeof singleEntry === "object" && !Array.isArray(singleEntry)) {
+        const v = singleEntry.k;
+        data[key] = v === null || v === undefined ? "" : v;
+      } else {
+        data[key] = rawValue;
+      }
+    } catch {
+      data[key] = rawValue;
+    }
+  }
+  return data;
+}
+function parseFrontmatterBlock(raw) {
+  const match = raw.match(/^---\r?\n([\s\S]*?)\r?\n---(?:\r\n|\r|\n|$)([\s\S]*)$/);
+  if (match) {
+    const frontmatter = match[1].replace(/\r/g, "");
+    const content = match[2];
+    return {
+      frontmatter,
+      content,
+      bodyStartLine: countLines(raw.slice(0, match[0].length - match[2].length)) + 1
+    };
+  }
+  const emptyMatch = raw.match(/^---\r?\n---(?:\r\n|\r|\n)([\s\S]*)$/);
+  if (emptyMatch) {
+    return { frontmatter: "", content: emptyMatch[1], bodyStartLine: 3 };
+  }
+  return null;
+}
+function countLines(text) {
+  if (text.length === 0)
+    return 0;
+  return text.split(/\r?\n/).length - 1;
+}
+var init_frontmatter = __esm(() => {
+  init_dist();
+});
+
+// src/core/asset/markdown.ts
+function parseMarkdownToc(content) {
+  const lines = content.split(/\r?\n/);
+  const headings = [];
+  const parsed = parseFrontmatter(content);
+  const start = parsed.frontmatter ? parsed.bodyStartLine - 1 : 0;
+  let inFence = false;
+  for (let i = start;i < lines.length; i++) {
+    if (/^\s*(`{3,}|~{3,})/.test(lines[i])) {
+      inFence = !inFence;
+      continue;
+    }
+    if (inFence)
+      continue;
+    const match = lines[i].match(/^(#{1,6})\s+(.+)$/);
+    if (match) {
+      headings.push({
+        level: match[1].length,
+        text: match[2].replace(/\s+#+\s*$/, "").trim(),
+        line: i + 1
+      });
+    }
+  }
+  return { headings, totalLines: lines.length };
+}
+var init_markdown = __esm(() => {
+  init_frontmatter();
+});
+
+// src/core/warn.ts
+import fs2 from "fs";
+function isVerbose() {
+  const env = process.env.AKM_VERBOSE?.trim().toLowerCase();
+  if (env === "1" || env === "true" || env === "yes" || env === "on")
+    return true;
+  if (env === "0" || env === "false" || env === "no" || env === "off")
+    return false;
+  return verbose;
+}
+function appendToLogFile(level, args) {
+  if (!logFilePath)
+    return;
+  const ts = new Date().toISOString();
+  const msg = args.map((a) => typeof a === "string" ? a : JSON.stringify(a)).join(" ");
+  try {
+    fs2.appendFileSync(logFilePath, `[${ts}] [${level}] ${msg}
+`);
+  } catch (e) {
+    process.stderr.write(`[akm:warn] log-file write failed (${logFilePath}): ${e}
+`);
+    process.stderr.write(`[${ts}] [${level}] ${msg}
+`);
+  }
+}
+function warn(...args) {
+  appendToLogFile("WARN", args);
+  if (!quiet) {
+    console.warn(...args);
+  }
+}
+function error(...args) {
+  appendToLogFile("ERROR", args);
+  if (!quiet) {
+    console.error(...args);
+  }
+}
+function warnVerbose(...args) {
+  if (isVerbose()) {
+    warn(...args);
+  }
+}
+var quiet = false, verbose = false, logFilePath;
+var init_warn = () => {};
+
+// src/indexer/walk/file-context.ts
+var renderers;
+var init_file_context = __esm(() => {
+  init_frontmatter();
+  init_common();
+  renderers = new Map;
+});
+
+// src/indexer/passes/metadata-contributors.ts
+function registerMetadataContributor(contributor) {
+  contributors.push(contributor);
+}
+var contributors;
+var init_metadata_contributors = __esm(() => {
+  contributors = [];
+});
+
+// src/indexer/passes/metadata.ts
+import fs3 from "fs";
+function extractDescriptionFromComments(filePath) {
+  let content;
+  try {
+    content = fs3.readFileSync(filePath, "utf8");
+  } catch {
+    return null;
+  }
+  const lines = content.split(/\r?\n/).slice(0, 50);
+  const blockStart = lines.findIndex((l) => /^\s*\/\*\*/.test(l));
+  if (blockStart >= 0) {
+    const desc = [];
+    for (let i = blockStart;i < lines.length; i++) {
+      const line = lines[i];
+      if (i > blockStart && /\*\//.test(line))
+        break;
+      const cleaned = line.replace(/^\s*\/?\*\*?\s?/, "").replace(/\*\/\s*$/, "").trim();
+      if (cleaned)
+        desc.push(cleaned);
+    }
+    if (desc.length > 0)
+      return desc.join(" ");
+  }
+  let start = 0;
+  if (lines[0]?.startsWith("#!"))
+    start = 1;
+  const hashLines = [];
+  for (let i = start;i < lines.length; i++) {
+    const line = lines[i].trim();
+    if (line.startsWith("#") && !line.startsWith("#!")) {
+      hashLines.push(line.replace(/^#+\s*/, "").trim());
+    } else if (line === "") {} else {
+      break;
+    }
+  }
+  if (hashLines.length > 0)
+    return hashLines.join(" ");
+  return null;
+}
+var KNOWN_QUALITY_VALUES, warnedUnknownQualityValues, WIKI_INFRA_FILES;
+var init_metadata = __esm(() => {
+  init_asset_spec();
+  init_frontmatter();
+  init_common();
+  init_warn();
+  init_file_context();
+  init_metadata_contributors();
+  KNOWN_QUALITY_VALUES = new Set(["generated", "curated", "enriched", "proposed"]);
+  warnedUnknownQualityValues = new Set;
+  WIKI_INFRA_FILES = new Set(["schema.md", "index.md", "log.md"]);
+});
+
+// src/core/asset/asset-ref.ts
+import path from "path";
+function parseAssetRef(ref) {
+  const trimmed = ref.trim();
+  if (!trimmed)
+    throw new UsageError("Empty ref.", "MISSING_REQUIRED_ARGUMENT");
+  let origin;
+  let body = trimmed;
+  const boundary = trimmed.indexOf("//");
+  if (boundary >= 0) {
+    origin = trimmed.slice(0, boundary);
+    body = trimmed.slice(boundary + 2);
+    if (!origin)
+      throw new UsageError("Empty origin in ref.", "MISSING_REQUIRED_ARGUMENT");
+  }
+  const colon = body.indexOf(":");
+  if (colon <= 0) {
+    throw new UsageError(`Invalid ref "${trimmed}". Expected [origin//]type:name, e.g. skill:deploy or knowledge:guide.md`, "MISSING_REQUIRED_ARGUMENT");
+  }
+  const rawType = body.slice(0, colon);
+  const rawName = body.slice(colon + 1);
+  if (rawType === "vault") {
+    throw new UsageError("The `vault` asset type was removed in 0.9.0 \u2014 use `env:` (whole .env config) or `secret:` (a single value).", "MISSING_REQUIRED_ARGUMENT");
+  }
+  const resolvedType = TYPE_ALIASES[rawType] ?? rawType;
+  if (!isAssetType(resolvedType)) {
+    throw new UsageError(`Invalid asset type: "${rawType}".`, "MISSING_REQUIRED_ARGUMENT");
+  }
+  validateName(rawName);
+  const name = normalizeName(rawName);
+  return { type: resolvedType, name, origin: origin || undefined };
+}
+function validateName(name) {
+  if (!name)
+    throw new UsageError("Empty asset name.", "MISSING_REQUIRED_ARGUMENT");
+  if (name.includes("\x00"))
+    throw new UsageError("Null byte in asset name.", "MISSING_REQUIRED_ARGUMENT");
+  if (/^[A-Za-z]:/.test(name))
+    throw new UsageError("Windows drive path in asset name.", "MISSING_REQUIRED_ARGUMENT");
+  const normalized = path.posix.normalize(name.replace(/\\/g, "/"));
+  if (path.posix.isAbsolute(normalized))
+    throw new UsageError("Absolute path in asset name.", "MISSING_REQUIRED_ARGUMENT");
+  if (normalized === ".." || normalized.startsWith("../")) {
+    throw new UsageError("Path traversal in asset name.", "MISSING_REQUIRED_ARGUMENT");
+  }
+  const segments = normalized.split("/");
+  if (segments.some((seg) => seg === "." || seg === "..")) {
+    throw new UsageError("Asset name cannot contain relative path segments.", "MISSING_REQUIRED_ARGUMENT");
+  }
+}
+function normalizeName(name) {
+  return path.posix.normalize(name.replace(/\\/g, "/"));
+}
+var TYPE_ALIASES;
+var init_asset_ref = __esm(() => {
+  init_common();
+  init_errors();
+  TYPE_ALIASES = {
+    environment: "env"
+  };
+});
+
+// src/workflows/schema.ts
 var WORKFLOW_SCHEMA_VERSION = 1;
 
 // src/workflows/validator.ts
@@ -8198,6 +8149,7 @@ function sortErrors(errors2) {
 var WORKFLOW_TITLE_PREFIX = "Workflow:", STEP_PREFIX = "Step:", STEP_ID_LINE, BULLET_LINE, SUBSECTION_INSTRUCTIONS = "Instructions", SUBSECTION_COMPLETION_CRITERIA = "Completion Criteria";
 var init_parser = __esm(() => {
   init_dist();
+  init_frontmatter();
   init_markdown();
   init_validator();
   STEP_ID_LINE = /^Step ID:\s+(.+?)\s*$/;
@@ -8387,6 +8339,7 @@ function applyTaskMetadata(entry, ctx) {
 }
 var init_renderers = __esm(() => {
   init_env();
+  init_frontmatter();
   init_markdown();
   init_common();
   init_metadata();
@@ -8816,29 +8769,126 @@ var init_database = __esm(() => {
   nodeRequire = createRequire(import.meta.url);
 });
 
-// src/storage/engines/sqlite-migrations.ts
-function ensureMigrationsTable(db) {
-  db.exec(`
-    CREATE TABLE IF NOT EXISTS schema_migrations (
-      id         TEXT    PRIMARY KEY,
-      applied_at TEXT    NOT NULL DEFAULT (datetime('now'))
-    );
-  `);
+// src/storage/engines/sqlite-migrations.ts
+function ensureMigrationsTable(db) {
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS schema_migrations (
+      id         TEXT    PRIMARY KEY,
+      applied_at TEXT    NOT NULL DEFAULT (datetime('now'))
+    );
+  `);
+}
+function runMigrations(db, migrations, opts) {
+  ensureMigrationsTable(db);
+  opts?.bootstrap?.(db);
+  const appliedRows = db.prepare("SELECT id FROM schema_migrations").all();
+  const applied = new Set(appliedRows.map((r) => r.id));
+  for (const migration of migrations) {
+    if (applied.has(migration.id))
+      continue;
+    db.transaction(() => {
+      db.exec(migration.up);
+      db.prepare("INSERT INTO schema_migrations (id) VALUES (?)").run(migration.id);
+    })();
+  }
+}
+
+// src/runtime.ts
+import { createHash } from "crypto";
+import { createWriteStream, statfsSync } from "fs";
+import { createRequire as createRequire2 } from "module";
+function sha256Hex(data) {
+  return createHash("sha256").update(data).digest("hex");
+}
+function statfsType(path5) {
+  try {
+    return statfsSync(path5).type;
+  } catch {
+    return;
+  }
+}
+function sleepSync(ms) {
+  if (isBun2) {
+    bunGlobal().sleepSync(ms);
+    return;
+  }
+  Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, ms);
+}
+function bunGlobal() {
+  return globalThis.Bun;
+}
+var isBun2, nodeRequire2, mainPath;
+var init_runtime = __esm(() => {
+  isBun2 = !!process.versions?.bun;
+  nodeRequire2 = createRequire2(import.meta.url);
+  mainPath = isBun2 ? bunGlobal().main : process.argv[1];
+});
+
+// src/storage/sqlite-pragmas.ts
+function resolveJournalMode(raw) {
+  if (raw === undefined)
+    return "WAL";
+  const normalized = raw.trim().toUpperCase();
+  if (normalized === "")
+    return "WAL";
+  if (VALID_MODES.has(normalized)) {
+    return normalized;
+  }
+  warnInvalidJournalModeOnce(raw);
+  return "WAL";
+}
+function resolveConfiguredJournalMode() {
+  return resolveJournalMode(process.env.AKM_SQLITE_JOURNAL_MODE);
+}
+function warnInvalidJournalModeOnce(raw) {
+  if (warnedInvalid)
+    return;
+  warnedInvalid = true;
+  warn(`[akm] invalid AKM_SQLITE_JOURNAL_MODE=${JSON.stringify(raw)} \u2014 using WAL (valid: WAL, DELETE, TRUNCATE)`);
 }
-function runMigrations(db, migrations, opts) {
-  ensureMigrationsTable(db);
-  opts?.bootstrap?.(db);
-  const appliedRows = db.prepare("SELECT id FROM schema_migrations").all();
-  const applied = new Set(appliedRows.map((r) => r.id));
-  for (const migration of migrations) {
-    if (applied.has(migration.id))
-      continue;
-    db.transaction(() => {
-      db.exec(migration.up);
-      db.prepare("INSERT INTO schema_migrations (id) VALUES (?)").run(migration.id);
-    })();
+function isNetworkFilesystem(fsType) {
+  if (fsType === undefined)
+    return false;
+  return NETWORK_FS_MAGICS.has(fsType);
+}
+function applyStandardPragmas(db, opts = {}) {
+  let mode = resolveConfiguredJournalMode();
+  if (mode === "WAL" && opts.dataDir) {
+    const probe = opts.fsTypeProbe ?? statfsType;
+    if (isNetworkFilesystem(probe(opts.dataDir))) {
+      mode = "DELETE";
+      warnNetworkFallbackOnce(opts.dataDir);
+    }
   }
+  db.exec("PRAGMA busy_timeout = 30000");
+  db.exec(`PRAGMA journal_mode = ${mode}`);
+  if (opts.foreignKeys !== false) {
+    db.exec("PRAGMA foreign_keys = ON");
+  }
+  if (mode !== "WAL") {
+    db.exec("PRAGMA synchronous = FULL");
+  }
+  return mode;
+}
+function warnNetworkFallbackOnce(dataDir) {
+  if (warnedNetworkFallback)
+    return;
+  warnedNetworkFallback = true;
+  warn(`[akm] network filesystem detected at ${dataDir} \u2014 WAL unsupported, using DELETE journal mode`);
 }
+var VALID_MODES, warnedInvalid = false, warnedNetworkFallback = false, FS_MAGIC_NFS = 26985, FS_MAGIC_SMB = 20859, FS_MAGIC_CIFS = 4283649346, FS_MAGIC_SMB2 = 4266872130, FS_MAGIC_FUSE = 1702057286, NETWORK_FS_MAGICS;
+var init_sqlite_pragmas = __esm(() => {
+  init_warn();
+  init_runtime();
+  VALID_MODES = new Set(["WAL", "DELETE", "TRUNCATE"]);
+  NETWORK_FS_MAGICS = new Set([
+    FS_MAGIC_NFS,
+    FS_MAGIC_SMB,
+    FS_MAGIC_CIFS,
+    FS_MAGIC_SMB2,
+    FS_MAGIC_FUSE
+  ]);
+});
 
 // src/core/assert.ts
 function assertNever(x, context) {
@@ -8882,12 +8932,17 @@ var init_improve_types = () => {};
 // src/core/state-db.ts
 var exports_state_db = {};
 __export(exports_state_db, {
+  withImmediateTransaction: () => withImmediateTransaction,
   upsertTaskHistory: () => upsertTaskHistory,
   upsertProposal: () => upsertProposal,
   upsertExtractedSession: () => upsertExtractedSession,
+  upsertConsolidationJudged: () => upsertConsolidationJudged,
+  upsertBodyEmbeddings: () => upsertBodyEmbeddings,
   shouldSkipAlreadyExtractedSession: () => shouldSkipAlreadyExtractedSession,
   runMigrations: () => runMigrations2,
+  recordRecombineInduction: () => recordRecombineInduction,
   recordImproveRun: () => recordImproveRun,
+  recordFsProposalsImport: () => recordFsProposalsImport,
   readStateEvents: () => readStateEvents,
   queryTaskHistory: () => queryTaskHistory,
   queryImproveRuns: () => queryImproveRuns,
@@ -8896,19 +8951,32 @@ __export(exports_state_db, {
   purgeOldEvents: () => purgeOldEvents,
   proposalToRowValues: () => proposalToRowValues,
   proposalRowToProposal: () => proposalRowToProposal,
+  persistPhaseThreshold: () => persistPhaseThreshold,
   openStateDatabase: () => openStateDatabase,
+  markRecombineHypothesisPromoted: () => markRecombineHypothesisPromoted,
   listStateProposals: () => listStateProposals,
+  listStateProposalIdsByPrefix: () => listStateProposalIdsByPrefix,
+  listProposalGateDecisions: () => listProposalGateDecisions,
   listExistingTableNames: () => listExistingTableNames,
+  insertProposalIfAbsent: () => insertProposalIfAbsent,
   insertEvent: () => insertEvent,
   importEventsJsonl: () => importEventsJsonl,
+  hasImportedFsProposals: () => hasImportedFsProposals,
   getTaskHistoryRuns: () => getTaskHistoryRuns,
   getTaskHistory: () => getTaskHistory,
   getStateProposal: () => getStateProposal,
   getStateDbPath: () => getStateDbPath,
+  getRecombineHypothesis: () => getRecombineHypothesis,
+  getPhaseThreshold: () => getPhaseThreshold,
   getExtractedSessionsMap: () => getExtractedSessionsMap,
   getExtractedSession: () => getExtractedSession,
+  getConsolidationJudgedMap: () => getConsolidationJudgedMap,
+  getBodyEmbeddings: () => getBodyEmbeddings,
   eventRowToEnvelope: () => eventRowToEnvelope,
+  embeddingToBlob: () => embeddingToBlob,
+  decayUnseenRecombineHypotheses: () => decayUnseenRecombineHypotheses,
   computeImproveRunMetrics: () => computeImproveRunMetrics,
+  blobToEmbedding: () => blobToEmbedding,
   REGISTRY_INDEX_CACHE_DDL: () => REGISTRY_INDEX_CACHE_DDL
 });
 import fs5 from "fs";
@@ -8923,9 +8991,7 @@ function openStateDatabase(dbPath) {
     fs5.mkdirSync(dir, { recursive: true });
   }
   const db = openDatabase(resolvedPath);
-  db.exec("PRAGMA journal_mode = WAL");
-  db.exec("PRAGMA foreign_keys = ON");
-  db.exec("PRAGMA busy_timeout = 5000");
+  applyStandardPragmas(db, { dataDir: dir });
   runMigrations2(db);
   return db;
 }
@@ -8972,7 +9038,11 @@ function proposalRowToProposal(row) {
       content: row.content,
       ...frontmatter !== undefined ? { frontmatter } : {}
     },
-    ...meta.review !== undefined ? { review: meta.review } : {}
+    ...meta.review !== undefined ? { review: meta.review } : {},
+    ...typeof meta.confidence === "number" ? { confidence: meta.confidence } : {},
+    ...meta.gateDecision !== undefined ? { gateDecision: meta.gateDecision } : {},
+    ...typeof meta.backupContent === "string" ? { backupContent: meta.backupContent } : {},
+    ...typeof meta.eligibilitySource === "string" ? { eligibilitySource: meta.eligibilitySource } : {}
   };
 }
 function proposalToRowValues(proposal, stashDir) {
@@ -8981,6 +9051,14 @@ function proposalToRowValues(proposal, stashDir) {
     metaObj.sourceRun = proposal.sourceRun;
   if (proposal.review !== undefined)
     metaObj.review = proposal.review;
+  if (proposal.confidence !== undefined)
+    metaObj.confidence = proposal.confidence;
+  if (proposal.gateDecision !== undefined)
+    metaObj.gateDecision = proposal.gateDecision;
+  if (proposal.backupContent !== undefined)
+    metaObj.backupContent = proposal.backupContent;
+  if (proposal.eligibilitySource !== undefined)
+    metaObj.eligibilitySource = proposal.eligibilitySource;
   return {
     id: proposal.id,
     stash_dir: stashDir,
@@ -9074,15 +9152,78 @@ function listStateProposals(db, options = {}) {
   const where = conditions.length > 0 ? `WHERE ${conditions.join(" AND ")}` : "";
   const rows = db.prepare(`SELECT id, stash_dir, ref, status, source, created_at, updated_at,
               content, frontmatter_json, metadata_json
-       FROM proposals ${where} ORDER BY created_at ASC`).all(...params);
+       FROM proposals ${where} ORDER BY created_at ASC, rowid ASC`).all(...params);
   return rows.map(proposalRowToProposal);
 }
-function getStateProposal(db, id) {
-  const row = db.prepare(`SELECT id, stash_dir, ref, status, source, created_at, updated_at,
+function listProposalGateDecisions(db) {
+  const rows = db.prepare("SELECT metadata_json FROM proposals ORDER BY created_at ASC, rowid ASC").all();
+  const decisions = [];
+  for (const row of rows) {
+    let meta;
+    try {
+      meta = JSON.parse(row.metadata_json);
+    } catch {
+      continue;
+    }
+    const decision = meta.gateDecision;
+    if (decision && typeof decision === "object" && typeof decision.outcome === "string") {
+      decisions.push(decision);
+    }
+  }
+  decisions.sort((a, b) => new Date(a.decidedAt).getTime() - new Date(b.decidedAt).getTime());
+  return decisions;
+}
+function getPhaseThreshold(db, phase) {
+  const row = db.prepare("SELECT threshold FROM improve_gate_thresholds WHERE phase = ?").get(phase);
+  return row?.threshold;
+}
+function persistPhaseThreshold(db, phase, threshold) {
+  db.prepare(`INSERT OR REPLACE INTO improve_gate_thresholds (phase, threshold, updated_at)
+     VALUES (?, ?, ?)`).run(phase, Math.round(threshold), Date.now());
+}
+function getStateProposal(db, id, stashDir) {
+  const sql = `SELECT id, stash_dir, ref, status, source, created_at, updated_at,
               content, frontmatter_json, metadata_json
-       FROM proposals WHERE id = ?`).get(id);
+       FROM proposals WHERE id = ?${stashDir ? " AND stash_dir = ?" : ""}`;
+  const row = stashDir ? db.prepare(sql).get(id, stashDir) : db.prepare(sql).get(id);
   return row ? proposalRowToProposal(row) : undefined;
 }
+function listStateProposalIdsByPrefix(db, stashDir, idPrefix) {
+  const escaped = idPrefix.replace(/[\\%_]/g, (ch) => `\\${ch}`);
+  const rows = db.prepare(`SELECT id FROM proposals
+       WHERE stash_dir = ? AND status = 'pending' AND id LIKE ? ESCAPE '\\'
+       ORDER BY id ASC`).all(stashDir, `${escaped}%`);
+  return rows.map((r) => r.id);
+}
+function hasImportedFsProposals(db, stashDir) {
+  return Boolean(db.prepare("SELECT 1 FROM proposal_fs_imports WHERE stash_dir = ?").get(stashDir));
+}
+function recordFsProposalsImport(db, stashDir, importedCount) {
+  db.prepare("INSERT OR REPLACE INTO proposal_fs_imports (stash_dir, imported_at, imported_count) VALUES (?, ?, ?)").run(stashDir, new Date().toISOString(), importedCount);
+}
+function insertProposalIfAbsent(db, proposal, stashDir) {
+  const v = proposalToRowValues(proposal, stashDir);
+  const result = db.prepare(`
+      INSERT OR IGNORE INTO proposals
+        (id, stash_dir, ref, status, source, created_at, updated_at, content, frontmatter_json, metadata_json)
+      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `).run(v.id, v.stash_dir, v.ref, v.status, v.source, v.created_at, v.updated_at, v.content, v.frontmatter_json, v.metadata_json);
+  const changes = result.changes ?? 0;
+  return Number(changes) > 0;
+}
+function withImmediateTransaction(db, fn) {
+  db.exec("BEGIN IMMEDIATE");
+  try {
+    const result = fn();
+    db.exec("COMMIT");
+    return result;
+  } catch (err) {
+    try {
+      db.exec("ROLLBACK");
+    } catch {}
+    throw err;
+  }
+}
 function upsertTaskHistory(db, row) {
   db.prepare(`
     INSERT OR IGNORE INTO task_history
@@ -9241,9 +9382,10 @@ function upsertExtractedSession(db, input) {
   db.prepare(`
     INSERT OR REPLACE INTO extract_sessions_seen
       (harness, session_id, processed_at, session_ended_at, outcome,
-       candidate_count, proposal_count, rationale, source_run, metadata_json)
-    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
-  `).run(input.harness, input.sessionId, input.processedAt, endedAtIso, input.outcome, input.candidateCount, input.proposalCount, input.rationale ?? null, input.sourceRun ?? null, JSON.stringify(input.metadata ?? {}));
+       candidate_count, proposal_count, rationale, source_run, metadata_json,
+       content_hash)
+    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+  `).run(input.harness, input.sessionId, input.processedAt, endedAtIso, input.outcome, input.candidateCount, input.proposalCount, input.rationale ?? null, input.sourceRun ?? null, JSON.stringify(input.metadata ?? {}), input.contentHash);
 }
 function getExtractedSession(db, harness, sessionId) {
   const row = db.prepare("SELECT * FROM extract_sessions_seen WHERE harness = ? AND session_id = ?").get(harness, sessionId);
@@ -9264,16 +9406,114 @@ function getExtractedSessionsMap(db, harness, sessionIds) {
   }
   return out;
 }
-function shouldSkipAlreadyExtractedSession(prior, liveSessionEndedAtMs) {
+function shouldSkipAlreadyExtractedSession(prior, currentContentHash) {
   if (!prior)
     return false;
-  if (typeof liveSessionEndedAtMs !== "number" || !Number.isFinite(liveSessionEndedAtMs)) {
-    return true;
-  }
-  const priorMs = prior.session_ended_at ? Date.parse(prior.session_ended_at) : Number.NaN;
-  if (!Number.isFinite(priorMs))
+  if (prior.content_hash == null)
     return false;
-  return liveSessionEndedAtMs <= priorMs;
+  return prior.content_hash === currentContentHash;
+}
+function getConsolidationJudgedMap(db, entryKeys) {
+  const out = new Map;
+  if (entryKeys.length === 0)
+    return out;
+  const CHUNK = 500;
+  for (let i = 0;i < entryKeys.length; i += CHUNK) {
+    const chunk = entryKeys.slice(i, i + CHUNK);
+    const placeholders = chunk.map(() => "?").join(",");
+    const rows = db.prepare(`SELECT * FROM consolidation_judged WHERE entry_key IN (${placeholders})`).all(...chunk);
+    for (const row of rows)
+      out.set(row.entry_key, row);
+  }
+  return out;
+}
+function upsertConsolidationJudged(db, input) {
+  db.prepare(`
+    INSERT OR REPLACE INTO consolidation_judged
+      (entry_key, content_hash, judged_at, outcome)
+    VALUES (?, ?, ?, ?)
+  `).run(input.entryKey, input.contentHash, input.judgedAt, input.outcome);
+}
+function recordRecombineInduction(db, input) {
+  const row = db.prepare(`
+      INSERT INTO recombine_hypotheses
+        (hypothesis_ref, signature, member_key, consecutive_count, first_seen_at, last_seen_at, last_run)
+      VALUES (?, ?, ?, 1, ?, ?, ?)
+      ON CONFLICT(hypothesis_ref) DO UPDATE SET
+        consecutive_count = consecutive_count + (CASE WHEN last_run IS excluded.last_run THEN 0 ELSE 1 END),
+        last_seen_at = excluded.last_seen_at,
+        last_run = excluded.last_run,
+        signature = excluded.signature,
+        member_key = excluded.member_key
+      RETURNING consecutive_count
+    `).get(input.hypothesisRef, input.signature, input.memberKey, input.seenAt, input.seenAt, input.run);
+  return row?.consecutive_count ?? 0;
+}
+function getRecombineHypothesis(db, hypothesisRef) {
+  const row = db.prepare("SELECT * FROM recombine_hypotheses WHERE hypothesis_ref = ?").get(hypothesisRef);
+  return row ?? undefined;
+}
+function markRecombineHypothesisPromoted(db, hypothesisRef, promotedAt) {
+  db.prepare("UPDATE recombine_hypotheses SET promoted_at = ?, consecutive_count = 0 WHERE hypothesis_ref = ?").run(promotedAt, hypothesisRef);
+}
+function decayUnseenRecombineHypotheses(db, currentRun, seenRefs) {
+  if (seenRefs.length === 0) {
+    const res2 = db.prepare("UPDATE recombine_hypotheses SET consecutive_count = 0 WHERE promoted_at IS NULL AND (last_run IS NULL OR last_run != ?) AND consecutive_count != 0").run(currentRun);
+    return Number(res2.changes);
+  }
+  if (seenRefs.length > 900) {
+    const res2 = db.prepare("UPDATE recombine_hypotheses SET consecutive_count = 0 WHERE promoted_at IS NULL AND (last_run IS NULL OR last_run != ?) AND consecutive_count != 0").run(currentRun);
+    return Number(res2.changes);
+  }
+  const placeholders = seenRefs.map(() => "?").join(",");
+  const res = db.prepare(`UPDATE recombine_hypotheses SET consecutive_count = 0
+       WHERE promoted_at IS NULL
+         AND (last_run IS NULL OR last_run != ?)
+         AND consecutive_count != 0
+         AND hypothesis_ref NOT IN (${placeholders})`).run(currentRun, ...seenRefs);
+  return Number(res.changes);
+}
+function embeddingToBlob(vec) {
+  const f32 = new Float32Array(vec);
+  return new Uint8Array(f32.buffer);
+}
+function blobToEmbedding(blob) {
+  const f32 = new Float32Array(blob.buffer, blob.byteOffset, blob.byteLength / 4);
+  return Array.from(f32);
+}
+function getBodyEmbeddings(db, contentHashes, expectedModelId) {
+  const out = new Map;
+  if (contentHashes.length === 0)
+    return out;
+  const firstRow = db.prepare("SELECT model_id FROM body_embeddings LIMIT 1").get();
+  if (firstRow && firstRow.model_id !== expectedModelId) {
+    db.exec("DELETE FROM body_embeddings");
+    return out;
+  }
+  const CHUNK = 500;
+  for (let i = 0;i < contentHashes.length; i += CHUNK) {
+    const chunk = contentHashes.slice(i, i + CHUNK);
+    const placeholders = chunk.map(() => "?").join(",");
+    const rows = db.prepare(`SELECT content_hash, embedding FROM body_embeddings WHERE content_hash IN (${placeholders})`).all(...chunk);
+    for (const row of rows) {
+      out.set(row.content_hash, blobToEmbedding(row.embedding));
+    }
+  }
+  return out;
+}
+function upsertBodyEmbeddings(db, entries) {
+  if (entries.length === 0)
+    return;
+  const now = Date.now();
+  const stmt = db.prepare(`
+    INSERT OR REPLACE INTO body_embeddings (content_hash, embedding, model_id, created_at)
+    VALUES (?, ?, ?, ?)
+  `);
+  db.transaction(() => {
+    for (const { contentHash, embedding, modelId } of entries) {
+      stmt.run(contentHash, embeddingToBlob(embedding), modelId, now);
+    }
+  })();
 }
 var MIGRATIONS, REGISTRY_INDEX_CACHE_DDL = `
   CREATE TABLE IF NOT EXISTS registry_index_cache (
@@ -9289,6 +9529,7 @@ var MIGRATIONS, REGISTRY_INDEX_CACHE_DDL = `
 `;
 var init_state_db = __esm(() => {
   init_database();
+  init_sqlite_pragmas();
   init_improve_types();
   init_paths();
   init_warn();
@@ -9363,7 +9604,9 @@ var init_state_db = __esm(() => {
       --
       -- Extensible (metadata_json) columns:
       --   metadata_json TEXT      \u2014 JSON object for future proposal fields.
-      --                             Current fields stored here: sourceRun, review.
+      --                             Current fields stored here: sourceRun,
+      --                             review, confidence, gateDecision (#577),
+      --                             backupContent, eligibilitySource.
       --
       -- ADD COLUMN extension points (future migrations):
       --   ALTER TABLE proposals ADD COLUMN source_run TEXT DEFAULT NULL;
@@ -9550,6 +9793,127 @@ var init_state_db = __esm(() => {
       CREATE INDEX IF NOT EXISTS idx_extract_sessions_processed
         ON extract_sessions_seen(processed_at);
     `
+    },
+    {
+      id: "005-proposal-fs-imports",
+      up: `
+      CREATE TABLE IF NOT EXISTS proposal_fs_imports (
+        stash_dir      TEXT    PRIMARY KEY,
+        imported_at    TEXT    NOT NULL,
+        imported_count INTEGER NOT NULL DEFAULT 0
+      );
+    `
+    },
+    {
+      id: "006-proposals-pending-ref-source",
+      up: `
+      CREATE INDEX IF NOT EXISTS idx_proposals_stash_status_ref_source
+        ON proposals(stash_dir, status, ref, source);
+    `
+    },
+    {
+      id: "007-consolidation-judged",
+      up: `
+      CREATE TABLE IF NOT EXISTS consolidation_judged (
+        entry_key    TEXT    PRIMARY KEY,
+        content_hash TEXT    NOT NULL,
+        judged_at    TEXT    NOT NULL,
+        outcome      TEXT    NOT NULL
+      );
+    `
+    },
+    {
+      id: "008-body-embeddings",
+      up: `
+      CREATE TABLE IF NOT EXISTS body_embeddings (
+        content_hash TEXT    PRIMARY KEY,
+        embedding    BLOB    NOT NULL,
+        model_id     TEXT    NOT NULL,
+        created_at   INTEGER NOT NULL
+      );
+    `
+    },
+    {
+      id: "009-asset-salience",
+      up: `
+      CREATE TABLE IF NOT EXISTS asset_salience (
+        asset_ref          TEXT    PRIMARY KEY,
+        encoding_salience  REAL    NOT NULL DEFAULT 0.5,
+        outcome_salience   REAL    NOT NULL DEFAULT 0.0,
+        retrieval_salience REAL    NOT NULL DEFAULT 0.0,
+        rank_score         REAL    NOT NULL DEFAULT 0.0,
+        consecutive_no_ops INTEGER NOT NULL DEFAULT 0,
+        updated_at         INTEGER NOT NULL DEFAULT 0
+      );
+
+      -- Hot path: sort / filter by rank_score for selector queries.
+      CREATE INDEX IF NOT EXISTS idx_asset_salience_rank
+        ON asset_salience(rank_score DESC);
+    `
+    },
+    {
+      id: "010-asset-outcome",
+      up: `
+      CREATE TABLE IF NOT EXISTS asset_outcome (
+        asset_ref                TEXT    PRIMARY KEY,
+        last_retrieved_at        INTEGER NOT NULL DEFAULT 0,
+        retrieval_count          INTEGER NOT NULL DEFAULT 0,
+        expected_retrieval_rate  REAL    NOT NULL DEFAULT 0.0,
+        negative_feedback_count  INTEGER NOT NULL DEFAULT 0,
+        accepted_change_count    INTEGER NOT NULL DEFAULT 0,
+        review_pressure          INTEGER NOT NULL DEFAULT 0,
+        outcome_score            REAL    NOT NULL DEFAULT 0.0,
+        updated_at               INTEGER NOT NULL DEFAULT 0
+      );
+
+      -- Hot path: sort assets by review_pressure DESC for #613 admission.
+      CREATE INDEX IF NOT EXISTS idx_asset_outcome_review_pressure
+        ON asset_outcome(review_pressure DESC);
+
+      -- Secondary: sort by outcome_score DESC for outcomeSalience reads.
+      CREATE INDEX IF NOT EXISTS idx_asset_outcome_score
+        ON asset_outcome(outcome_score DESC);
+    `
+    },
+    {
+      id: "011-asset-salience-homeostatic-demoted-at",
+      up: `
+      ALTER TABLE asset_salience ADD COLUMN homeostatic_demoted_at INTEGER DEFAULT NULL;
+    `
+    },
+    {
+      id: "012-improve-gate-thresholds",
+      up: `
+      CREATE TABLE IF NOT EXISTS improve_gate_thresholds (
+        phase       TEXT    NOT NULL PRIMARY KEY,
+        threshold   INTEGER NOT NULL,
+        updated_at  INTEGER NOT NULL
+      );
+    `
+    },
+    {
+      id: "013-extract-sessions-content-hash",
+      up: `
+      ALTER TABLE extract_sessions_seen ADD COLUMN content_hash TEXT DEFAULT NULL;
+    `
+    },
+    {
+      id: "014-recombine-hypotheses",
+      up: `
+      CREATE TABLE IF NOT EXISTS recombine_hypotheses (
+        hypothesis_ref    TEXT PRIMARY KEY,
+        signature         TEXT NOT NULL,
+        member_key        TEXT NOT NULL,
+        consecutive_count INTEGER NOT NULL DEFAULT 0,
+        first_seen_at     TEXT NOT NULL,
+        last_seen_at      TEXT NOT NULL,
+        last_run          TEXT,
+        promoted_at       TEXT,
+        metadata_json     TEXT NOT NULL DEFAULT '{}'
+      );
+      CREATE INDEX IF NOT EXISTS idx_recombine_hypotheses_last_seen
+        ON recombine_hypotheses(last_seen_at);
+    `
     }
   ];
 });
@@ -9593,29 +9957,6 @@ var init_types = __esm(() => {
   init_warn();
 });
 
-// src/runtime.ts
-import { createHash } from "crypto";
-import { createRequire as createRequire2 } from "module";
-function sha256Hex(data) {
-  return createHash("sha256").update(data).digest("hex");
-}
-function sleepSync(ms) {
-  if (isBun2) {
-    bunGlobal().sleepSync(ms);
-    return;
-  }
-  Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, ms);
-}
-function bunGlobal() {
-  return globalThis.Bun;
-}
-var isBun2, nodeRequire2, mainPath;
-var init_runtime = __esm(() => {
-  isBun2 = !!process.versions?.bun;
-  nodeRequire2 = createRequire2(import.meta.url);
-  mainPath = isBun2 ? bunGlobal().main : process.argv[1];
-});
-
 // src/indexer/search/search-fields.ts
 function buildSearchFields(entry) {
   const name = entry.name.replace(/[-_]/g, " ").toLowerCase();
@@ -10238,6 +10579,9 @@ var init_inline_refs = __esm(() => {
 import fs9 from "fs";
 import os from "os";
 import path8 from "path";
+function claudeProjectsDir() {
+  return process.env.AKM_CLAUDE_PROJECTS_DIR ?? path8.join(os.homedir(), ".claude", "projects");
+}
 function parseClaudeEvent(entry, sessionId, filePath, fallbackTsMs) {
   if (!entry || typeof entry !== "object")
     return;
@@ -10294,11 +10638,15 @@ function parseClaudeEvent(entry, sessionId, filePath, fallbackTsMs) {
 class ClaudeCodeProvider {
   name = "claude-code";
   isAvailable() {
-    return fs9.existsSync(CLAUDE_PROJECTS_DIR);
+    return fs9.existsSync(claudeProjectsDir());
+  }
+  watchRoots() {
+    const dir = claudeProjectsDir();
+    return fs9.existsSync(dir) ? [dir] : [];
   }
   *readEvents(input) {
     try {
-      for (const jsonlPath of this.#walkJsonl(CLAUDE_PROJECTS_DIR)) {
+      for (const jsonlPath of this.#walkJsonl(claudeProjectsDir())) {
         const stat = fs9.statSync(jsonlPath);
         if (stat.mtimeMs < input.sinceMs)
           continue;
@@ -10326,7 +10674,7 @@ class ClaudeCodeProvider {
     }
   }
   listSessions(input = {}) {
-    const root = input.location ?? CLAUDE_PROJECTS_DIR;
+    const root = input.location ?? claudeProjectsDir();
     const sinceMs = input.sinceMs ?? 0;
     const summaries = [];
     try {
@@ -10460,16 +10808,14 @@ class ClaudeCodeProvider {
         const full = path8.join(dir, entry.name);
         if (entry.isDirectory())
           yield* this.#walkJsonl(full);
-        else if (entry.name.endsWith(".jsonl"))
+        else if (entry.name.endsWith(".jsonl") && entry.name !== "journal.jsonl")
           yield full;
       }
     } catch {}
   }
 }
-var CLAUDE_PROJECTS_DIR;
 var init_session_log = __esm(() => {
   init_inline_refs();
-  CLAUDE_PROJECTS_DIR = path8.join(os.homedir(), ".claude", "projects");
 });
 
 // src/integrations/harnesses/claude/index.ts
@@ -10532,6 +10878,10 @@ class OpenCodeProvider {
   isAvailable() {
     return fs10.existsSync(this.#baseDir);
   }
+  watchRoots() {
+    const sessionRoot = path9.join(this.#baseDir, "storage", "session");
+    return fs10.existsSync(sessionRoot) ? [sessionRoot] : [];
+  }
   *readEvents(input) {
     const candidates = [this.#baseDir, path9.join(this.#baseDir, "log")];
     for (const dir of candidates) {
@@ -15392,7 +15742,7 @@ var init_config_types = __esm(() => {
 });
 
 // src/core/config/config-schema.ts
-var positiveInt, nonNegativeNumber, nonEmptyString, httpUrl, LlmCapabilitiesSchema, LlmConnectionConfigSchema, LlmProfileConfigSchema, EmbeddingOllamaOptionsSchema, EmbeddingConnectionConfigSchema, AgentPlatformSchema, AgentProfileConfigSchema, ImproveProcessConfigSchema, ImproveProfileProcessesSchema, ImproveProfileConfigSchema, ProfilesSchema, DefaultsSchema, SourceConfigEntryOptionsSchema, SourceConfigEntrySchema, RegistryConfigEntrySchema, KitSourceSchema, InstalledStashEntrySchema, OutputConfigSchema, SearchGraphBoostSchema, SearchConfigSchema, FeedbackConfigSchema, ImproveUtilityDecaySchema, ImproveConfigSchema, GRAPH_EXTRACTION_INCLUDE_TYPES_ALLOWED, INDEX_PASS_PROVIDER_KEYS, INDEX_PASS_KNOWN_KEYS, IndexPassConfigSchema, MetadataEnhanceSchema, StalenessDetectionSchema, IndexConfigSchema, SetupTaskSchedulesSchema, SetupConfigSchema, AkmConfigShape, AkmConfigBaseSchema, AkmConfigSchema;
+var positiveInt, nonNegativeNumber, nonEmptyString, httpUrl, LlmCapabilitiesSchema, LlmConnectionConfigSchema, LlmProfileConfigSchema, EmbeddingOllamaOptionsSchema, EmbeddingConnectionConfigSchema, AgentPlatformSchema, AgentProfileConfigSchema, ImproveProcessConfigSchema, ImproveProfileProcessesSchema, ImproveProfileConfigSchema, ProfilesSchema, DefaultsSchema, SourceConfigEntryOptionsSchema, SourceConfigEntrySchema, RegistryConfigEntrySchema, KitSourceSchema, InstalledStashEntrySchema, OutputConfigSchema, SearchGraphBoostSchema, SearchConfigSchema, FeedbackConfigSchema, ImproveUtilityDecaySchema, ImproveCalibrationSchema, ImproveExplorationSchema, ImproveSalienceSchema, ImproveConfigSchema, GRAPH_EXTRACTION_INCLUDE_TYPES_ALLOWED, INDEX_PASS_PROVIDER_KEYS, INDEX_PASS_KNOWN_KEYS, IndexPassConfigSchema, MetadataEnhanceSchema, StalenessDetectionSchema, IndexConfigSchema, SetupTaskSchedulesSchema, SetupConfigSchema, AkmConfigShape, AkmConfigBaseSchema, AkmConfigSchema;
 var init_config_schema = __esm(() => {
   init_zod();
   init_config_types();
@@ -15454,14 +15804,63 @@ var init_config_schema = __esm(() => {
     timeoutMs: exports_external.union([positiveInt, exports_external.null()]).optional(),
     allowedTypes: exports_external.array(exports_external.string().min(1)).optional(),
     minPoolSize: exports_external.number().int().min(0).optional(),
+    dedup: exports_external.object({
+      enabled: exports_external.boolean().optional(),
+      cosineThreshold: exports_external.number().min(0).max(1).optional(),
+      cosineCandidateLimit: exports_external.number().int().positive().optional()
+    }).strict().optional(),
+    judgedCache: exports_external.object({ enabled: exports_external.boolean().optional() }).strict().optional(),
     qualityGate: exports_external.object({ enabled: exports_external.boolean().optional() }).strict().optional(),
     contradictionDetection: exports_external.object({ enabled: exports_external.boolean().optional() }).strict().optional(),
     defaultSince: exports_external.string().min(1).optional(),
     maxTotalChars: positiveInt.optional(),
+    minContentChars: exports_external.number().int().min(0).optional(),
     maxChunkSize: exports_external.number().int().min(1).max(50).optional(),
+    incrementalSince: exports_external.string().optional(),
+    limit: positiveInt.optional(),
+    neighborsPerChanged: exports_external.number().int().min(1).optional(),
+    requirePlannedRefs: exports_external.boolean().optional(),
+    dueDays: exports_external.number().int().min(0).optional(),
+    maxPerRun: positiveInt.optional(),
+    minPendingCount: exports_external.number().int().min(0).optional(),
     minNewSessions: exports_external.number().int().min(0).optional(),
+    maxSessionsPerRun: exports_external.number().int().min(0).optional(),
     indexSessions: exports_external.boolean().optional(),
     minSessionDuration: exports_external.number().min(0).optional(),
+    p90ChunkSecondsDefault: exports_external.number().finite().positive().optional(),
+    homeostaticDemotion: exports_external.object({
+      enabled: exports_external.boolean().optional(),
+      staleDays: exports_external.number().int().min(0).optional(),
+      demotionFactor: exports_external.number().min(0).max(1).optional()
+    }).strict().optional(),
+    schemaSimilarity: exports_external.object({
+      enabled: exports_external.boolean().optional(),
+      epsilon: exports_external.number().min(0).max(1).optional(),
+      confidencePenalty: exports_external.number().min(0).max(1).optional()
+    }).strict().optional(),
+    hotProbation: exports_external.object({
+      enabled: exports_external.boolean().optional()
+    }).strict().optional(),
+    antiCollapse: exports_external.object({
+      enabled: exports_external.boolean().optional(),
+      maxGeneration: exports_external.number().int().min(1).optional(),
+      lexicalDiversityCheck: exports_external.boolean().optional(),
+      randomClusterFraction: exports_external.number().min(0).max(1).optional()
+    }).strict().optional(),
+    cls: exports_external.object({
+      enabled: exports_external.boolean().optional(),
+      adjacentCount: exports_external.number().int().min(1).optional()
+    }).strict().optional(),
+    fidelityCheck: exports_external.object({
+      enabled: exports_external.boolean().optional()
+    }).strict().optional(),
+    minClusterSize: exports_external.number().int().min(2).optional(),
+    maxClustersPerRun: positiveInt.optional(),
+    relatednessSource: exports_external.enum(["tags", "graph", "both"]).optional(),
+    confirmThreshold: exports_external.number().int().min(1).optional(),
+    minRecurrence: exports_external.number().int().min(2).optional(),
+    maxProposalsPerRun: positiveInt.optional(),
+    emitAs: exports_external.enum(["workflow", "skill"]).optional(),
     applyMode: exports_external.enum(["queue", "promote"]).optional(),
     policy: exports_external.string().min(1).optional(),
     maxAcceptsPerRun: positiveInt.optional(),
@@ -15480,7 +15879,10 @@ var init_config_schema = __esm(() => {
     memoryInference: ImproveProcessConfigSchema.optional(),
     graphExtraction: ImproveProcessConfigSchema.optional(),
     validation: ImproveProcessConfigSchema.optional(),
-    triage: ImproveProcessConfigSchema.optional()
+    triage: ImproveProcessConfigSchema.optional(),
+    proactiveMaintenance: ImproveProcessConfigSchema.optional(),
+    recombine: ImproveProcessConfigSchema.optional(),
+    procedural: ImproveProcessConfigSchema.optional()
   }).passthrough().superRefine((val, ctx) => {
     const raw = val;
     if ("feedbackDistillation" in raw) {
@@ -15498,7 +15900,10 @@ var init_config_schema = __esm(() => {
       "graphExtraction",
       "validation",
       "extract",
-      "triage"
+      "triage",
+      "proactiveMaintenance",
+      "recombine",
+      "procedural"
     ]);
     for (const k of Object.keys(raw)) {
       if (!allowed.has(k)) {
@@ -15515,6 +15920,7 @@ var init_config_schema = __esm(() => {
     processes: ImproveProfileProcessesSchema.optional(),
     autoAccept: nonNegativeNumber.optional(),
     limit: positiveInt.optional(),
+    symmetricValence: exports_external.boolean().optional(),
     sync: exports_external.object({
       enabled: exports_external.boolean().optional(),
       push: exports_external.boolean().optional(),
@@ -15595,6 +16001,7 @@ var init_config_schema = __esm(() => {
   }).strict();
   SearchConfigSchema = exports_external.object({
     minScore: nonNegativeNumber.optional(),
+    defaultExcludeTypes: exports_external.array(nonEmptyString).optional(),
     curateRerank: exports_external.object({ enabled: exports_external.boolean().optional() }).strict().optional(),
     graphBoost: SearchGraphBoostSchema.optional()
   }).strict();
@@ -15606,9 +16013,29 @@ var init_config_schema = __esm(() => {
     halfLifeDays: exports_external.number().finite().min(0.1).optional(),
     feedbackStabilityBoost: exports_external.number().finite().min(1).optional()
   }).strict();
+  ImproveCalibrationSchema = exports_external.object({
+    autoTune: exports_external.boolean().optional(),
+    minThreshold: exports_external.number().int().min(0).max(100).optional(),
+    maxThreshold: exports_external.number().int().min(0).max(100).optional(),
+    maxStep: positiveInt.optional(),
+    minSamples: nonNegativeNumber.optional(),
+    targetAcceptRate: exports_external.number().finite().min(0).max(1).optional()
+  }).strict();
+  ImproveExplorationSchema = exports_external.object({
+    enabled: exports_external.boolean().optional(),
+    budgetFraction: exports_external.number().finite().min(0).max(1).optional()
+  }).strict();
+  ImproveSalienceSchema = exports_external.object({
+    outcomeWeightEnabled: exports_external.boolean().optional(),
+    salienceThreshold: exports_external.number().min(0).max(1).optional(),
+    replayBudget: exports_external.number().int().min(0).optional()
+  }).strict();
   ImproveConfigSchema = exports_external.object({
     utilityDecay: ImproveUtilityDecaySchema.optional(),
-    eventRetentionDays: nonNegativeNumber.optional()
+    eventRetentionDays: nonNegativeNumber.optional(),
+    calibration: ImproveCalibrationSchema.optional(),
+    exploration: ImproveExplorationSchema.optional(),
+    salience: ImproveSalienceSchema.optional()
   }).strict();
   GRAPH_EXTRACTION_INCLUDE_TYPES_ALLOWED = [
     "memory",
@@ -15991,9 +16418,9 @@ function maybeAutoMigrateConfigFile(configPath, text) {
       "\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501"
     ].join(`
 `);
-    process.stderr.write(`${banner}
+    process.stderr?.write?.(`${banner}
 `);
-    process.stdout.write(`${banner}
+    process.stdout?.write?.(`${banner}
 `);
   } catch (err) {
     throw new ConfigError(`Failed to write migrated config to ${configPath}: ${err instanceof Error ? err.message : String(err)}`, "INVALID_CONFIG_FILE", "Check filesystem permissions, free space, and disk health. To skip auto-migration, set AKM_NO_AUTO_MIGRATE=1.");
@@ -16237,6 +16664,7 @@ __export(exports_db, {
   getMeta: () => getMeta,
   getLlmCacheEntry: () => getLlmCacheEntry,
   getLlmCacheEntriesByRefs: () => getLlmCacheEntriesByRefs,
+  getIndexedFilePaths: () => getIndexedFilePaths,
   getIndexDirState: () => getIndexDirState,
   getEntryRefRowsForStashRoot: () => getEntryRefRowsForStashRoot,
   getEntryIdByFilePath: () => getEntryIdByFilePath,
@@ -16245,6 +16673,7 @@ __export(exports_db, {
   getEntryByRef: () => getEntryByRef,
   getEntryById: () => getEntryById,
   getEntriesByDir: () => getEntriesByDir,
+  getEntitiesByEntryIds: () => getEntitiesByEntryIds,
   getEmbeddingCount: () => getEmbeddingCount,
   getEmbeddableEntryCount: () => getEmbeddableEntryCount,
   getDerivedForParent: () => getDerivedForParent,
@@ -16279,9 +16708,7 @@ function openDatabase2(dbPath, options) {
     fs12.mkdirSync(dir, { recursive: true });
   }
   const db = openDatabase(resolvedPath);
-  db.exec("PRAGMA journal_mode = WAL");
-  db.exec("PRAGMA busy_timeout = 5000");
-  db.exec("PRAGMA foreign_keys = ON");
+  applyStandardPragmas(db, { dataDir: dir });
   loadVecExtension(db);
   const resolvedDim = options?.embeddingDim ?? resolveConfiguredEmbeddingDim();
   ensureSchema(db, resolvedDim, { dataDir: dir });
@@ -16302,10 +16729,9 @@ function resolveConfiguredEmbeddingDim() {
 }
 function openExistingDatabase(dbPath) {
   const resolvedPath = dbPath ?? getDbPath();
+  const dir = path11.dirname(resolvedPath);
   const db = openDatabase(resolvedPath);
-  db.exec("PRAGMA journal_mode = WAL");
-  db.exec("PRAGMA busy_timeout = 5000");
-  db.exec("PRAGMA foreign_keys = ON");
+  applyStandardPragmas(db, { dataDir: dir });
   loadVecExtension(db);
   return db;
 }
@@ -16470,6 +16896,7 @@ function ensureSchema(db, embeddingDim, options) {
      CREATE INDEX IF NOT EXISTS idx_llm_cache_updated
        ON llm_enrichment_cache(updated_at);
   `);
+  migrateGraphFilesSchema(db);
   db.exec(`
     CREATE TABLE IF NOT EXISTS graph_meta (
       stash_root          TEXT PRIMARY KEY,
@@ -16493,7 +16920,6 @@ function ensureSchema(db, embeddingDim, options) {
     );
 
     CREATE TABLE IF NOT EXISTS graph_files (
-      entry_id          INTEGER PRIMARY KEY REFERENCES entries(id) ON DELETE CASCADE,
       stash_root        TEXT NOT NULL,
       file_path         TEXT NOT NULL,
       file_order        INTEGER NOT NULL,
@@ -16503,26 +16929,34 @@ function ensureSchema(db, embeddingDim, options) {
       status            TEXT NOT NULL DEFAULT 'extracted',
       reason            TEXT,
       extraction_run_id TEXT,
-      UNIQUE(stash_root, file_path)
+      PRIMARY KEY (stash_root, file_path, body_hash)
     );
 
+    CREATE UNIQUE INDEX IF NOT EXISTS idx_graph_files_path
+      ON graph_files(stash_root, file_path);
+
     CREATE INDEX IF NOT EXISTS idx_graph_files_stash_order
       ON graph_files(stash_root, file_order);
 
     CREATE TABLE IF NOT EXISTS graph_file_entities (
-      entry_id     INTEGER NOT NULL REFERENCES graph_files(entry_id) ON DELETE CASCADE,
-      entity_order INTEGER NOT NULL,
       stash_root   TEXT NOT NULL,
+      file_path    TEXT NOT NULL,
+      body_hash    TEXT NOT NULL,
+      entity_order INTEGER NOT NULL,
       entity_norm  TEXT NOT NULL,
       entity       TEXT NOT NULL,
-      PRIMARY KEY (entry_id, entity_order)
+      PRIMARY KEY (stash_root, file_path, body_hash, entity_order),
+      FOREIGN KEY (stash_root, file_path, body_hash)
+        REFERENCES graph_files(stash_root, file_path, body_hash) ON DELETE CASCADE
     );
 
     CREATE INDEX IF NOT EXISTS idx_graph_file_entities_entity_norm
       ON graph_file_entities(stash_root, entity_norm);
 
     CREATE TABLE IF NOT EXISTS graph_file_relations (
-      entry_id       INTEGER NOT NULL REFERENCES graph_files(entry_id) ON DELETE CASCADE,
+      stash_root     TEXT NOT NULL,
+      file_path      TEXT NOT NULL,
+      body_hash      TEXT NOT NULL,
       relation_order INTEGER NOT NULL,
       from_entity_norm TEXT NOT NULL,
       from_entity    TEXT NOT NULL,
@@ -16530,9 +16964,12 @@ function ensureSchema(db, embeddingDim, options) {
       to_entity      TEXT NOT NULL,
       relation_type  TEXT,
       confidence     REAL,
-      PRIMARY KEY (entry_id, relation_order)
+      PRIMARY KEY (stash_root, file_path, body_hash, relation_order),
+      FOREIGN KEY (stash_root, file_path, body_hash)
+        REFERENCES graph_files(stash_root, file_path, body_hash) ON DELETE CASCADE
     );
   `);
+  migrateGraphDataFromLegacy(db);
   db.exec(`
     CREATE TABLE IF NOT EXISTS entries_fts_dirty (
       entry_id INTEGER PRIMARY KEY
@@ -16748,6 +17185,67 @@ function ensureDerivedFromColumn(db) {
     db.exec("CREATE INDEX IF NOT EXISTS idx_entries_derived_from ON entries(derived_from)");
   }, "entries table may not exist on a brand-new DB before CREATE \u2014 caller is responsible");
 }
+function tableExists(db, name) {
+  const row = db.prepare("SELECT 1 FROM sqlite_master WHERE type='table' AND name=? LIMIT 1").get(name);
+  return row !== undefined && row !== null;
+}
+function migrateGraphFilesSchema(db) {
+  bestEffort(() => {
+    const cols = db.prepare("PRAGMA table_info(graph_files)").all();
+    const isLegacyShape = cols.some((c) => c.name === "entry_id");
+    if (!isLegacyShape)
+      return;
+    db.exec("DROP TABLE IF EXISTS graph_file_relations_legacy");
+    db.exec("DROP TABLE IF EXISTS graph_file_entities_legacy");
+    db.exec("DROP TABLE IF EXISTS graph_files_legacy");
+    db.exec("ALTER TABLE graph_files RENAME TO graph_files_legacy");
+    if (tableExists(db, "graph_file_entities")) {
+      db.exec("ALTER TABLE graph_file_entities RENAME TO graph_file_entities_legacy");
+    }
+    if (tableExists(db, "graph_file_relations")) {
+      db.exec("ALTER TABLE graph_file_relations RENAME TO graph_file_relations_legacy");
+    }
+  }, "graph_files may not exist on a brand-new DB before CREATE \u2014 caller is responsible");
+}
+function migrateGraphDataFromLegacy(db) {
+  if (!tableExists(db, "graph_files_legacy"))
+    return;
+  let migratedFiles = 0;
+  bestEffort(() => {
+    db.transaction(() => {
+      const res = db.prepare(`INSERT OR IGNORE INTO graph_files
+             (stash_root, file_path, body_hash, file_order, file_type, confidence, status, reason, extraction_run_id)
+           SELECT stash_root, file_path, body_hash, file_order, file_type, confidence, status, reason, extraction_run_id
+             FROM graph_files_legacy
+            WHERE body_hash IS NOT NULL AND body_hash != ''`).run();
+      migratedFiles = Number(res.changes);
+      if (tableExists(db, "graph_file_entities_legacy")) {
+        db.exec(`INSERT OR IGNORE INTO graph_file_entities
+             (stash_root, file_path, body_hash, entity_order, entity_norm, entity)
+           SELECT gf.stash_root, gf.file_path, gf.body_hash, e.entity_order, e.entity_norm, e.entity
+             FROM graph_file_entities_legacy e
+             JOIN graph_files_legacy gf ON gf.entry_id = e.entry_id
+            WHERE gf.body_hash IS NOT NULL AND gf.body_hash != ''`);
+      }
+      if (tableExists(db, "graph_file_relations_legacy")) {
+        db.exec(`INSERT OR IGNORE INTO graph_file_relations
+             (stash_root, file_path, body_hash, relation_order, from_entity_norm, from_entity, to_entity_norm, to_entity, relation_type, confidence)
+           SELECT gf.stash_root, gf.file_path, gf.body_hash, r.relation_order, r.from_entity_norm, r.from_entity, r.to_entity_norm, r.to_entity, r.relation_type, r.confidence
+             FROM graph_file_relations_legacy r
+             JOIN graph_files_legacy gf ON gf.entry_id = r.entry_id
+            WHERE gf.body_hash IS NOT NULL AND gf.body_hash != ''`);
+      }
+    })();
+  }, "graph data migration is best-effort; legacy tables are dropped regardless below");
+  bestEffort(() => {
+    db.exec("DROP TABLE IF EXISTS graph_file_relations_legacy");
+    db.exec("DROP TABLE IF EXISTS graph_file_entities_legacy");
+    db.exec("DROP TABLE IF EXISTS graph_files_legacy");
+  }, "drop legacy graph tables after migration");
+  if (migratedFiles > 0) {
+    warn(`[akm] graph index re-keyed (#624): migrated ${migratedFiles} extracted file(s) to the new schema \u2014 no re-extraction needed. Index + embeddings untouched.`);
+  }
+}
 function getDerivedForParent(db, parentRef) {
   if (!parentRef)
     return null;
@@ -16837,6 +17335,25 @@ function deleteRelatedRows(db, ids) {
     bestEffort(() => db.prepare(`DELETE FROM utility_scores_scoped WHERE entry_id IN (${placeholders})`).run(...chunk), "delete utility_scores_scoped for entries");
     bestEffort(() => db.prepare(`DELETE FROM usage_events WHERE entry_id IN (${placeholders})`).run(...chunk), "delete usage_events for entries");
   }
+  const affectedStashRoots = new Set;
+  for (let i = 0;i < numericIds.length; i += SQLITE_CHUNK_SIZE) {
+    const chunk = numericIds.slice(i, i + SQLITE_CHUNK_SIZE);
+    const placeholders = chunk.map(() => "?").join(",");
+    bestEffort(() => {
+      const rows = db.prepare(`SELECT DISTINCT stash_dir FROM entries WHERE id IN (${placeholders})`).all(...chunk);
+      for (const row of rows) {
+        if (row.stash_dir)
+          affectedStashRoots.add(row.stash_dir);
+      }
+    }, "resolve stash roots for graph_meta recompute");
+  }
+  for (const stashRoot of affectedStashRoots) {
+    bestEffort(() => db.prepare(`UPDATE graph_meta
+             SET extracted_files = (SELECT COUNT(*) FROM graph_files WHERE stash_root = ?),
+                 entity_count    = (SELECT COUNT(*) FROM graph_file_entities WHERE stash_root = ?),
+                 relation_count  = (SELECT COUNT(*) FROM graph_file_relations WHERE stash_root = ?)
+             WHERE stash_root = ?`).run(stashRoot, stashRoot, stashRoot, stashRoot), "sync graph_meta counts after entries delete");
+  }
 }
 function deleteEntriesByIds(db, ids) {
   if (ids.length === 0)
@@ -16966,17 +17483,17 @@ function searchBlobVec(db, queryEmbedding, k) {
     return [];
   }
 }
-function searchFts(db, query, limit, entryType) {
+function searchFts(db, query, limit, entryType, excludeTypes) {
   const ftsQuery = sanitizeFtsQuery(query);
   if (!ftsQuery)
     return [];
-  const exactResults = runFtsQuery(db, ftsQuery, limit, entryType);
+  const exactResults = runFtsQuery(db, ftsQuery, limit, entryType, excludeTypes);
   if (exactResults.length > 0)
     return exactResults;
   const prefixQuery = buildPrefixQuery(ftsQuery);
   if (!prefixQuery)
     return [];
-  return runFtsQuery(db, prefixQuery, limit, entryType);
+  return runFtsQuery(db, prefixQuery, limit, entryType, excludeTypes);
 }
 function buildPrefixQuery(ftsQuery) {
   const tokens = ftsQuery.split(/\s+/).filter(Boolean);
@@ -16992,9 +17509,10 @@ function buildPrefixQuery(ftsQuery) {
     return null;
   return prefixTokens.join(" ");
 }
-function runFtsQuery(db, ftsQuery, limit, entryType) {
+function runFtsQuery(db, ftsQuery, limit, entryType, excludeTypes) {
   let sql;
   let params;
+  const excludes = excludeTypes && excludeTypes.length > 0 ? excludeTypes : [];
   if (entryType && entryType !== "any") {
     sql = `
       SELECT e.id, e.file_path AS filePath, e.entry_json, e.search_text AS searchText,
@@ -17008,16 +17526,18 @@ function runFtsQuery(db, ftsQuery, limit, entryType) {
     `;
     params = [ftsQuery, entryType, limit];
   } else {
+    const excludeClause = excludes.length > 0 ? `AND e.entry_type NOT IN (${excludes.map(() => "?").join(", ")})` : "";
     sql = `
       SELECT e.id, e.file_path AS filePath, e.entry_json, e.search_text AS searchText,
              bm25(entries_fts, 0, 10.0, 5.0, 3.0, 2.0, 1.0) AS bm25Score
       FROM entries_fts f
       JOIN entries e ON e.id = f.entry_id
       WHERE entries_fts MATCH ?
+        ${excludeClause}
       ORDER BY bm25Score, e.id ASC
       LIMIT ?
     `;
-    params = [ftsQuery, limit];
+    params = [ftsQuery, ...excludes, limit];
   }
   try {
     const rows = db.prepare(sql).all(...params);
@@ -17073,12 +17593,16 @@ function parseEntryRows(rows, context) {
   }
   return entries;
 }
-function getAllEntries(db, entryType) {
+function getAllEntries(db, entryType, excludeTypes) {
   let sql;
   let params;
+  const excludes = excludeTypes && excludeTypes.length > 0 ? excludeTypes : [];
   if (entryType && entryType !== "any") {
     sql = "SELECT id, entry_key, dir_path, file_path, stash_dir, entry_json, search_text FROM entries WHERE entry_type = ?";
     params = [entryType];
+  } else if (excludes.length > 0) {
+    sql = `SELECT id, entry_key, dir_path, file_path, stash_dir, entry_json, search_text FROM entries WHERE entry_type NOT IN (${excludes.map(() => "?").join(", ")})`;
+    params = [...excludes];
   } else {
     sql = "SELECT id, entry_key, dir_path, file_path, stash_dir, entry_json, search_text FROM entries";
     params = [];
@@ -17086,6 +17610,33 @@ function getAllEntries(db, entryType) {
   const rows = db.prepare(sql).all(...params);
   return parseEntryRows(rows, "getAllEntries");
 }
+function getEntitiesByEntryIds(db, entryIds) {
+  const result = new Map;
+  if (entryIds.length === 0)
+    return result;
+  for (let i = 0;i < entryIds.length; i += SQLITE_CHUNK_SIZE) {
+    const chunk = entryIds.slice(i, i + SQLITE_CHUNK_SIZE);
+    const placeholders = chunk.map(() => "?").join(", ");
+    const rows = db.prepare(`SELECT e.id AS entry_id, gfe.entity_norm AS entity_norm
+           FROM entries e
+           JOIN graph_files gf
+             ON gf.stash_root = e.stash_dir AND gf.file_path = e.file_path
+           JOIN graph_file_entities gfe
+             ON gfe.stash_root = gf.stash_root
+            AND gfe.file_path = gf.file_path
+            AND gfe.body_hash = gf.body_hash
+          WHERE e.id IN (${placeholders})
+          ORDER BY e.id, gfe.entity_order`).all(...chunk);
+    for (const row of rows) {
+      const list = result.get(row.entry_id);
+      if (list)
+        list.push(row.entity_norm);
+      else
+        result.set(row.entry_id, [row.entity_norm]);
+    }
+  }
+  return result;
+}
 function findEntryIdByRef(db, ref) {
   const parsed = parseAssetRef(ref);
   const nameVariants = [parsed.name];
@@ -17136,6 +17687,10 @@ function getEntryIdByFilePath(db, filePath) {
   const row = db.prepare("SELECT id FROM entries WHERE file_path = ? LIMIT 1").get(filePath);
   return row?.id;
 }
+function getIndexedFilePaths(db) {
+  const rows = db.prepare("SELECT DISTINCT file_path FROM entries WHERE file_path IS NOT NULL AND file_path <> ''").all();
+  return new Set(rows.map((r) => r.file_path));
+}
 function getEntryFilePathById(db, id) {
   const row = db.prepare("SELECT file_path FROM entries WHERE id = ?").get(id);
   return row?.file_path;
@@ -17263,18 +17818,56 @@ function clearStaleCacheEntries(db) {
 function computeBodyHash(body) {
   return sha256Hex(body);
 }
+function bareRef(ref) {
+  try {
+    const parsed = parseAssetRef(ref);
+    return `${parsed.type}:${parsed.name}`;
+  } catch {
+    return ref;
+  }
+}
 function getRetrievalCounts(db, refs) {
   if (refs.length === 0)
     return new Map;
-  const result = new Map;
-  for (let i = 0;i < refs.length; i += SQLITE_CHUNK_SIZE) {
-    const chunk = refs.slice(i, i + SQLITE_CHUNK_SIZE);
+  const bareToInputs = new Map;
+  for (const ref of refs) {
+    const bare = bareRef(ref);
+    const existing = bareToInputs.get(bare);
+    if (existing)
+      existing.push(ref);
+    else
+      bareToInputs.set(bare, [ref]);
+  }
+  const bareForms = [...bareToInputs.keys()];
+  const countsByBare = new Map;
+  for (let i = 0;i < bareForms.length; i += SQLITE_CHUNK_SIZE) {
+    const chunk = bareForms.slice(i, i + SQLITE_CHUNK_SIZE);
     const placeholders = chunk.map(() => "?").join(", ");
-    const rows = db.prepare(`SELECT entry_ref, COUNT(*) AS cnt FROM usage_events
-         WHERE event_type IN ('search','show') AND entry_ref IN (${placeholders})
-         GROUP BY entry_ref`).all(...chunk);
-    for (const r of rows)
-      result.set(r.entry_ref, r.cnt);
+    const rows = db.prepare(`SELECT
+           CASE
+             WHEN instr(entry_ref, '//') > 0
+               THEN substr(entry_ref, instr(entry_ref, '//') + 2)
+             ELSE entry_ref
+           END AS bare_ref,
+           COUNT(*) AS cnt
+         FROM usage_events
+         WHERE event_type IN ('search','show','curate')
+           AND entry_ref IS NOT NULL
+           AND CASE
+                 WHEN instr(entry_ref, '//') > 0
+                   THEN substr(entry_ref, instr(entry_ref, '//') + 2)
+                 ELSE entry_ref
+               END IN (${placeholders})
+         GROUP BY bare_ref`).all(...chunk);
+    for (const r of rows) {
+      countsByBare.set(r.bare_ref, (countsByBare.get(r.bare_ref) ?? 0) + r.cnt);
+    }
+  }
+  const result = new Map;
+  for (const [bare, count] of countsByBare) {
+    for (const input of bareToInputs.get(bare) ?? []) {
+      result.set(input, count);
+    }
   }
   return result;
 }
@@ -17438,7 +18031,7 @@ function collectTagSetFromEntries(db, entryType) {
   }
   return tags;
 }
-var DB_VERSION = 17, EMBEDDING_DIM = 384, GRAPH_SCHEMA_VERSION = 3, vecStatus, VEC_DOCS_URL = "https://github.com/itlackey/akm/blob/main/docs/configuration.md#sqlite-vec-extension", VEC_FALLBACK_THRESHOLD = 1e4, vecInitWarnedDbs, SQLITE_CHUNK_SIZE = 500, upsertStmtsByDb, FEEDBACK_LR = 0.1, FEEDBACK_REWARD_POSITIVE = 1, FEEDBACK_REWARD_NEGATIVE = 0, MAX_NEG_DELTA_PER_CALL = 0.15, UTILITY_REVIEW_THRESHOLD = 0.5, HIGH_UTILITY_THRESHOLD = 0.5;
+var DB_VERSION = 17, EMBEDDING_DIM = 384, GRAPH_SCHEMA_VERSION = 4, vecStatus, VEC_DOCS_URL = "https://github.com/itlackey/akm/blob/main/docs/configuration.md#sqlite-vec-extension", VEC_FALLBACK_THRESHOLD = 1e4, vecInitWarnedDbs, SQLITE_CHUNK_SIZE = 500, upsertStmtsByDb, FEEDBACK_LR = 0.1, FEEDBACK_REWARD_POSITIVE = 1, FEEDBACK_REWARD_NEGATIVE = 0, MAX_NEG_DELTA_PER_CALL = 0.15, UTILITY_REVIEW_THRESHOLD = 0.5, HIGH_UTILITY_THRESHOLD = 0.5;
 var init_db = __esm(() => {
   init_asset_ref();
   init_best_effort();
@@ -17448,6 +18041,7 @@ var init_db = __esm(() => {
   init_types();
   init_runtime();
   init_database();
+  init_sqlite_pragmas();
   init_db_backup();
   vecStatus = new WeakMap;
   vecInitWarnedDbs = new WeakSet;
@@ -17457,13 +18051,13 @@ var init_db = __esm(() => {
 // src/indexer/db/graph-db.ts
 var exports_graph_db = {};
 __export(exports_graph_db, {
-  resolveEntryIdForPath: () => resolveEntryIdForPath,
   replaceStoredGraph: () => replaceStoredGraph,
   loadStoredGraphSnapshot: () => loadStoredGraphSnapshot,
   loadStoredGraphMeta: () => loadStoredGraphMeta,
   loadGraphMetaOnly: () => loadGraphMetaOnly,
   loadGraphFilesOnly: () => loadGraphFilesOnly,
-  loadGraphEntitiesByEntry: () => loadGraphEntitiesByEntry,
+  loadGraphEntitiesByPath: () => loadGraphEntitiesByPath,
+  hasGraphData: () => hasGraphData,
   deleteStoredGraph: () => deleteStoredGraph
 });
 import fs13 from "fs";
@@ -17486,17 +18080,6 @@ function uniqueSorted(values) {
 function normalizeEntity(value) {
   return value.trim().toLowerCase();
 }
-function resolveEntryIdForPath(db, stashRoot, filePath) {
-  try {
-    const row = db.prepare("SELECT id FROM entries WHERE stash_dir = ? AND file_path = ? LIMIT 1").get(stashRoot, filePath);
-    if (row)
-      return row.id;
-    const fallback = db.prepare("SELECT id FROM entries WHERE file_path = ? LIMIT 1").get(filePath);
-    return fallback?.id ?? null;
-  } catch {
-    return null;
-  }
-}
 function replaceStoredGraph(db, graph) {
   const upsertMeta = db.prepare(`INSERT INTO graph_meta (
        stash_root,
@@ -17536,21 +18119,21 @@ function replaceStoredGraph(db, graph) {
         cache_misses = excluded.cache_misses,
         truncation_count = excluded.truncation_count,
         failure_count = excluded.failure_count`);
-  const selectExisting = db.prepare("SELECT entry_id, file_path, body_hash FROM graph_files WHERE stash_root = ?");
-  const deleteFile = db.prepare("DELETE FROM graph_files WHERE entry_id = ?");
-  const deleteEntities = db.prepare("DELETE FROM graph_file_entities WHERE entry_id = ?");
-  const deleteRelations = db.prepare("DELETE FROM graph_file_relations WHERE entry_id = ?");
+  const selectExisting = db.prepare("SELECT file_path, body_hash, file_order FROM graph_files WHERE stash_root = ?");
+  const deleteFile = db.prepare("DELETE FROM graph_files WHERE stash_root = ? AND file_path = ? AND body_hash = ?");
+  const deleteEntities = db.prepare("DELETE FROM graph_file_entities WHERE stash_root = ? AND file_path = ? AND body_hash = ?");
+  const deleteRelations = db.prepare("DELETE FROM graph_file_relations WHERE stash_root = ? AND file_path = ? AND body_hash = ?");
   const insertFile = db.prepare(`INSERT INTO graph_files (
-       entry_id, stash_root, file_path, file_order, file_type, body_hash, confidence, status, reason, extraction_run_id
-     ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`);
+       stash_root, file_path, file_order, file_type, body_hash, confidence, status, reason, extraction_run_id
+     ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)`);
   const updateFileMeta = db.prepare(`UPDATE graph_files
        SET file_order = ?, file_type = ?, confidence = ?, status = ?, reason = ?, extraction_run_id = ?
-        WHERE entry_id = ?`);
-  const insertEntity = db.prepare(`INSERT INTO graph_file_entities (entry_id, entity_order, stash_root, entity_norm, entity)
-     VALUES (?, ?, ?, ?, ?)`);
+        WHERE stash_root = ? AND file_path = ? AND body_hash = ?`);
+  const insertEntity = db.prepare(`INSERT INTO graph_file_entities (stash_root, file_path, body_hash, entity_order, entity_norm, entity)
+     VALUES (?, ?, ?, ?, ?, ?)`);
   const insertRelation = db.prepare(`INSERT INTO graph_file_relations (
-       entry_id, relation_order, from_entity_norm, from_entity, to_entity_norm, to_entity, relation_type, confidence
-     ) VALUES (?, ?, ?, ?, ?, ?, ?, ?)`);
+       stash_root, file_path, body_hash, relation_order, from_entity_norm, from_entity, to_entity_norm, to_entity, relation_type, confidence
+     ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`);
   const quality = graph.quality;
   const telemetry = graph.telemetry;
   db.transaction(() => {
@@ -17559,44 +18142,35 @@ function replaceStoredGraph(db, graph) {
     const existingByPath = new Map;
     for (const row of existingRows)
       existingByPath.set(row.file_path, row);
-    let orphanCount = 0;
-    const presentEntryIds = new Set;
+    const presentPaths = new Set;
     for (const [fileOrder, node] of graph.files.entries()) {
       const bodyHash = node.bodyHash && node.bodyHash.length > 0 ? node.bodyHash : "";
-      const entryId = resolveEntryIdForPath(db, graph.stashRoot, node.path);
-      if (entryId == null) {
-        orphanCount += 1;
-        continue;
-      }
-      presentEntryIds.add(entryId);
+      presentPaths.add(node.path);
       const existing = existingByPath.get(node.path);
-      if (existing && existing.entry_id === entryId && existing.body_hash === bodyHash) {
-        updateFileMeta.run(fileOrder, node.type, node.confidence ?? null, node.status ?? (node.entities.length > 0 ? "extracted" : "empty"), node.reason ?? (node.entities.length > 0 ? "none" : "no_graph_content"), node.extractionRunId ?? telemetry?.extractionRunId ?? null, entryId);
+      if (existing && existing.body_hash === bodyHash) {
+        updateFileMeta.run(fileOrder, node.type, node.confidence ?? null, node.status ?? (node.entities.length > 0 ? "extracted" : "empty"), node.reason ?? (node.entities.length > 0 ? "none" : "no_graph_content"), node.extractionRunId ?? telemetry?.extractionRunId ?? null, graph.stashRoot, node.path, bodyHash);
         continue;
       }
       if (existing) {
-        deleteEntities.run(existing.entry_id);
-        deleteRelations.run(existing.entry_id);
-        deleteFile.run(existing.entry_id);
+        deleteEntities.run(graph.stashRoot, existing.file_path, existing.body_hash);
+        deleteRelations.run(graph.stashRoot, existing.file_path, existing.body_hash);
+        deleteFile.run(graph.stashRoot, existing.file_path, existing.body_hash);
       }
-      insertFile.run(entryId, graph.stashRoot, node.path, fileOrder, node.type, bodyHash, node.confidence ?? null, node.status ?? (node.entities.length > 0 ? "extracted" : "empty"), node.reason ?? (node.entities.length > 0 ? "none" : "no_graph_content"), node.extractionRunId ?? telemetry?.extractionRunId ?? null);
+      insertFile.run(graph.stashRoot, node.path, fileOrder, node.type, bodyHash, node.confidence ?? null, node.status ?? (node.entities.length > 0 ? "extracted" : "empty"), node.reason ?? (node.entities.length > 0 ? "none" : "no_graph_content"), node.extractionRunId ?? telemetry?.extractionRunId ?? null);
       for (const [entityOrder, entity] of node.entities.entries()) {
-        insertEntity.run(entryId, entityOrder, graph.stashRoot, normalizeEntity(entity), entity);
+        insertEntity.run(graph.stashRoot, node.path, bodyHash, entityOrder, normalizeEntity(entity), entity);
       }
       for (const [relationOrder, relation] of node.relations.entries()) {
-        insertRelation.run(entryId, relationOrder, normalizeEntity(relation.from), relation.from, normalizeEntity(relation.to), relation.to, relation.type ?? null, relation.confidence ?? null);
+        insertRelation.run(graph.stashRoot, node.path, bodyHash, relationOrder, normalizeEntity(relation.from), relation.from, normalizeEntity(relation.to), relation.to, relation.type ?? null, relation.confidence ?? null);
       }
     }
     for (const row of existingRows) {
-      if (!presentEntryIds.has(row.entry_id)) {
-        deleteEntities.run(row.entry_id);
-        deleteRelations.run(row.entry_id);
-        deleteFile.run(row.entry_id);
+      if (!presentPaths.has(row.file_path)) {
+        deleteEntities.run(graph.stashRoot, row.file_path, row.body_hash);
+        deleteRelations.run(graph.stashRoot, row.file_path, row.body_hash);
+        deleteFile.run(graph.stashRoot, row.file_path, row.body_hash);
       }
     }
-    if (orphanCount > 0) {
-      warn(`[graph] replaceStoredGraph: skipped ${orphanCount} file(s) with no resolvable entry under ${graph.stashRoot}.`);
-    }
   })();
 }
 function deleteStoredGraph(db, stashPath) {
@@ -17605,6 +18179,14 @@ function deleteStoredGraph(db, stashPath) {
     db.prepare("DELETE FROM graph_meta WHERE stash_root = ?").run(stashPath);
   })();
 }
+function hasGraphData(db, stashRoot, filePath) {
+  try {
+    const row = db.prepare("SELECT 1 AS present FROM graph_files WHERE stash_root = ? AND file_path = ? LIMIT 1").get(stashRoot, filePath);
+    return row !== undefined;
+  } catch {
+    return false;
+  }
+}
 function loadGraphMetaOnly(stashPath, db) {
   return loadStoredGraphMeta(stashPath, db);
 }
@@ -17612,12 +18194,11 @@ function loadGraphFilesOnly(stashPath, db) {
   try {
     return withReadableGraphDb(db, (readDb) => {
       try {
-        const rows = readDb.prepare(`SELECT entry_id, file_path, file_type, body_hash, confidence, status, reason
+        const rows = readDb.prepare(`SELECT file_path, file_type, body_hash, confidence, status, reason
                 FROM graph_files
                 WHERE stash_root = ?
                 ORDER BY file_order`).all(stashPath);
         return rows.map((row) => ({
-          entryId: row.entry_id,
           path: row.file_path,
           type: row.file_type,
           bodyHash: row.body_hash,
@@ -17634,9 +18215,11 @@ function loadGraphFilesOnly(stashPath, db) {
     return [];
   }
 }
-function loadGraphEntitiesByEntry(db, entryId) {
+function loadGraphEntitiesByPath(db, stashRoot, filePath, bodyHash) {
   try {
-    const rows = db.prepare("SELECT entity FROM graph_file_entities WHERE entry_id = ? ORDER BY entity_order").all(entryId);
+    const rows = db.prepare(`SELECT entity FROM graph_file_entities
+          WHERE stash_root = ? AND file_path = ? AND body_hash = ?
+          ORDER BY entity_order`).all(stashRoot, filePath, bodyHash);
     return rows.map((r) => r.entity);
   } catch {
     return [];
@@ -17711,23 +18294,28 @@ function loadStoredGraphSnapshot(stashPath, db) {
       if (!meta)
         return null;
       try {
-        const fileRows = readDb.prepare(`SELECT entry_id, file_path, file_type, body_hash, confidence, status, reason, extraction_run_id
+        const fileRows = readDb.prepare(`SELECT file_path, file_type, body_hash, confidence, status, reason, extraction_run_id
               FROM graph_files
               WHERE stash_root = ?
               ORDER BY file_order`).all(stashPath);
-        const entityRows = readDb.prepare(`SELECT gfe.entry_id AS entry_id, gf.file_path AS file_path, gfe.entity AS entity
+        const entityRows = readDb.prepare(`SELECT gf.file_path AS file_path, gfe.entity AS entity
              FROM graph_file_entities gfe
-             JOIN graph_files gf ON gf.entry_id = gfe.entry_id
+             JOIN graph_files gf
+               ON gf.stash_root = gfe.stash_root
+              AND gf.file_path = gfe.file_path
+              AND gf.body_hash = gfe.body_hash
              WHERE gf.stash_root = ?
              ORDER BY gf.file_order, gfe.entity_order`).all(stashPath);
-        const relationRows = readDb.prepare(`SELECT gfr.entry_id AS entry_id,
-                    gf.file_path AS file_path,
+        const relationRows = readDb.prepare(`SELECT gf.file_path AS file_path,
                     gfr.from_entity AS from_entity,
                     gfr.to_entity AS to_entity,
                     gfr.relation_type AS relation_type,
                     gfr.confidence AS confidence
              FROM graph_file_relations gfr
-             JOIN graph_files gf ON gf.entry_id = gfr.entry_id
+             JOIN graph_files gf
+               ON gf.stash_root = gfr.stash_root
+              AND gf.file_path = gfr.file_path
+              AND gf.body_hash = gfr.body_hash
              WHERE gf.stash_root = ?
              ORDER BY gf.file_order, gfr.relation_order`).all(stashPath);
         const entitiesByPath = new Map;
@@ -17786,7 +18374,6 @@ function loadStoredGraphSnapshot(stashPath, db) {
 var init_graph_db = __esm(() => {
   init_errors();
   init_paths();
-  init_warn();
   init_db();
 });