@cerefox/memory 1.1.0-beta.1 → 1.1.0-beta.2

package/dist/bin/cerefox.js

@@ -7438,7 +7438,7 @@ var exports_meta = {};
 __export(exports_meta, {
   PKG_VERSION: () => PKG_VERSION
 });
-var PKG_VERSION = "1.1.0-beta.1";
+var PKG_VERSION = "1.1.0-beta.2";
 var init_meta = () => {};
 
 // ../../node_modules/.bun/tslib@2.8.1/node_modules/tslib/tslib.js
@@ -23362,9 +23362,12 @@ function loadEnv(opts = {}) {
   } catch {
     return { path: envPath, vars: 0 };
   }
+  const configDirNamed = (env2.CEREFOX_CONFIG_DIR ?? "").trim() !== "";
   let count = 0;
   for (const [k, v] of Object.entries(parseDotenv(content))) {
-    if (env2[k] === undefined) {
+    if (k === "CEREFOX_CONFIG_DIR")
+      continue;
+    if (env2[k] === undefined || configDirNamed) {
       env2[k] = v;
       count++;
     }
@@ -55186,6 +55189,36 @@ var init_audit_log = __esm(() => {
   };
 });
 
+// ../../_shared/mcp-tools/feature-flags.ts
+async function relationsEnabled(supabase) {
+  if (cached && Date.now() - cached.at < CACHE_TTL_MS)
+    return cached.value;
+  try {
+    const { data, error: error2 } = await supabase.rpc("cerefox_get_config", {
+      p_key: "relations_enabled"
+    });
+    if (error2)
+      throw new Error(error2.message);
+    const value = String(data ?? "").trim().toLowerCase() === "true";
+    cached = { value, at: Date.now() };
+    return value;
+  } catch {
+    return false;
+  }
+}
+function disabledToolMessage(name) {
+  return `${name} is part of the document-relations feature, which is off by default. ` + `Enable it with: cerefox config set relations_enabled true ` + `(deployment-wide; every access path picks it up).`;
+}
+var RELATION_TOOL_NAMES, CACHE_TTL_MS = 60000, cached = null;
+var init_feature_flags = __esm(() => {
+  RELATION_TOOL_NAMES = new Set([
+    "cerefox_set_relation",
+    "cerefox_delete_relation",
+    "cerefox_get_relations",
+    "cerefox_get_neighbors"
+  ]);
+});
+
 // ../../_shared/mcp-tools/types.ts
 var McpInvalidParams;
 var init_types3 = __esm(() => {
@@ -56281,9 +56314,21 @@ var init_set_document_projects = __esm(() => {
 });
 
 // ../../_shared/mcp-tools/index.ts
+async function listEnabledTools(supabase) {
+  const relations = await relationsEnabled(supabase);
+  return ALL_TOOLS.filter((t) => relations || !RELATION_TOOL_NAMES.has(t.name));
+}
+async function assertToolEnabled(supabase, name) {
+  if (!RELATION_TOOL_NAMES.has(name))
+    return;
+  if (await relationsEnabled(supabase))
+    return;
+  throw new McpInvalidParams(disabledToolMessage(name));
+}
 var ALL_TOOLS, TOOLS_BY_NAME;
 var init_mcp_tools = __esm(() => {
   init_audit_log();
+  init_feature_flags();
   init_relations();
   init_get_document();
   init_get_help();
@@ -56295,6 +56340,7 @@ var init_mcp_tools = __esm(() => {
   init_search();
   init_set_document_projects();
   init_types3();
+  init_types3();
   ALL_TOOLS = [
     searchTool,
     ingestTool,
@@ -56500,7 +56546,7 @@ __export(exports_util, {
   cleanRegex: () => cleanRegex,
   cleanEnum: () => cleanEnum,
   captureStackTrace: () => captureStackTrace,
-  cached: () => cached,
+  cached: () => cached2,
   assignProp: () => assignProp,
   assertNotEqual: () => assertNotEqual,
   assertNever: () => assertNever,
@@ -56537,7 +56583,7 @@ function jsonStringifyReplacer(_, value) {
     return value.toString();
   return value;
 }
-function cached(getter) {
+function cached2(getter) {
   const set = false;
   return {
     get value() {
@@ -56949,7 +56995,7 @@ var captureStackTrace, allowsEval, getParsedType2 = (data) => {
 }, propertyKeyTypes, primitiveTypes, NUMBER_FORMAT_RANGES, BIGINT_FORMAT_RANGES;
 var init_util2 = __esm(() => {
   captureStackTrace = Error.captureStackTrace ? Error.captureStackTrace : (..._args) => {};
-  allowsEval = cached(() => {
+  allowsEval = cached2(() => {
     if (typeof navigator !== "undefined" && navigator?.userAgent?.includes("Cloudflare")) {
       return false;
     }
@@ -58254,7 +58300,7 @@ var init_schemas = __esm(() => {
   });
   $ZodObject = /* @__PURE__ */ $constructor("$ZodObject", (inst, def) => {
     $ZodType.init(inst, def);
-    const _normalized = cached(() => {
+    const _normalized = cached2(() => {
       const keys = Object.keys(def.shape);
       for (const k of keys) {
         if (!(def.shape[k] instanceof $ZodType)) {
@@ -58474,7 +58520,7 @@ var init_schemas = __esm(() => {
       }
       return propValues;
     });
-    const disc = cached(() => {
+    const disc = cached2(() => {
       const opts = def.options;
       const map = new Map;
       for (const o of opts) {
@@ -69455,7 +69501,7 @@ function buildServer() {
   };
   const server = new Server({ name: SERVER_NAME, version: PKG_VERSION }, { capabilities: { tools: {} } });
   server.setRequestHandler(ListToolsRequestSchema, async () => ({
-    tools: ALL_TOOLS.map((t) => ({
+    tools: (await listEnabledTools(supabase)).map((t) => ({
       name: t.name,
       description: t.description,
       inputSchema: t.inputSchema
@@ -69468,6 +69514,7 @@ function buildServer() {
       throw new McpInvalidParams(`Unknown tool: ${name}`);
     }
     try {
+      await assertToolEnabled(supabase, name);
       const text = await tool.handler(supabase, args, ctx);
       return { content: [{ type: "text", text }] };
     } catch (err) {
@@ -69574,6 +69621,7 @@ async function fetchAllPages(makeQuery, batchSize = 200) {
 
 // src/cli/commands/backup.ts
 init_client();
+init_meta();
 function expandHome(path) {
   if (path === "~")
     return homedir2();
@@ -69587,18 +69635,67 @@ function utcStamp() {
   return d.getUTCFullYear().toString() + pad(d.getUTCMonth() + 1) + pad(d.getUTCDate()) + "T" + pad(d.getUTCHours()) + pad(d.getUTCMinutes()) + pad(d.getUTCSeconds()) + "Z";
 }
 async function action(options) {
-  const outDir = resolve(expandHome(options.outputDir ?? process.env.CEREFOX_BACKUP_DIR ?? "~/.cerefox/backups"));
+  const configuredDir = options.outputDir ?? process.env.CEREFOX_BACKUP_DIR;
+  const outDir = resolve(expandHome(configuredDir ?? "~/.cerefox/backups"));
+  if (configuredDir !== undefined && !configuredDir.startsWith("/") && !configuredDir.startsWith("~")) {
+    println(c.yellow("⚠ ") + `Backup directory "${configuredDir}" is relative — it resolves against the ` + "current working directory, so backups land in different places depending " + "on where you run this from.");
+    println(c.dim(`  Writing to: ${outDir}`));
+    println(c.dim("  Set an absolute path (e.g. ~/.cerefox/backups) to keep them together."));
+  }
   if (!existsSync2(outDir))
     mkdirSync(outDir, { recursive: true });
   const stamp = utcStamp();
   const filename = `cerefox-${stamp}${options.label ? "-" + options.label : ""}.json`;
   const dest = join2(outDir, filename);
   const client = getClient();
+  let schemaVersion = "unknown";
+  try {
+    schemaVersion = await client.rpc("cerefox_schema_version", {}) ?? "unknown";
+  } catch {}
+  const includeTrash = options.trash !== false;
+  const BASE_COLUMNS = "id, title, content_hash, source, metadata, total_chars, chunk_count, " + "review_status, created_at, updated_at, deleted_at";
+  const fetchDocs = (columns) => fetchAllPages((from, to) => {
+    const q = client.raw.from("cerefox_documents").select(columns);
+    return (includeTrash ? q : q.is("deleted_at", null)).order("created_at", { ascending: true }).order("id", { ascending: true }).range(from, to);
+  });
   let docs;
+  let lifecycleCaptured = true;
+  try {
+    docs = await fetchDocs(`${BASE_COLUMNS}, lifecycle_status`);
+  } catch (err) {
+    const message = err instanceof Error ? err.message : String(err);
+    if (!/lifecycle_status/.test(message)) {
+      throw systemError(`Document fetch failed: ${message}`);
+    }
+    lifecycleCaptured = false;
+    try {
+      docs = await fetchDocs(BASE_COLUMNS);
+    } catch (retryErr) {
+      throw systemError(`Document fetch failed: ${retryErr instanceof Error ? retryErr.message : String(retryErr)}`);
+    }
+    println(c.dim("  (server predates lifecycle_status — captured without it)"));
+  }
+  const trashedCount = docs.filter((d) => d.deleted_at != null).length;
+  let projects = [];
+  let memberships = [];
   try {
-    docs = await fetchAllPages((from, to) => client.raw.from("cerefox_documents").select("id, title, content_hash, source, metadata, total_chars, chunk_count, " + "review_status, created_at, updated_at, deleted_at").is("deleted_at", null).order("created_at", { ascending: true }).order("id", { ascending: true }).range(from, to));
+    projects = await fetchAllPages((from, to) => client.raw.from("cerefox_projects").select("id, name, description, created_at, updated_at").order("id", { ascending: true }).range(from, to));
+    memberships = await fetchAllPages((from, to) => client.raw.from("cerefox_document_projects").select("document_id, project_id").order("document_id", { ascending: true }).order("project_id", { ascending: true }).range(from, to));
   } catch (err) {
-    throw systemError(`Document fetch failed: ${err instanceof Error ? err.message : String(err)}`);
+    throw systemError(`Project/membership fetch failed: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  let relations = [];
+  try {
+    relations = await fetchAllPages((from, to) => client.raw.from("cerefox_document_relations").select("source_id, target_id, rel_type, metadata, author, author_type, created_at").order("source_id", { ascending: true }).order("target_id", { ascending: true }).order("rel_type", { ascending: true }).range(from, to));
+  } catch {}
+  {
+    const captured = new Set(docs.map((d) => d.id));
+    const before = memberships.length;
+    memberships = memberships.filter((m) => captured.has(m.document_id));
+    const dropped = before - memberships.length;
+    if (dropped > 0) {
+      println(c.dim(`  (skipped ${dropped} membership(s) belonging to trashed documents)`));
+    }
   }
   let chunkTotal = 0;
   const enriched = [];
@@ -69622,22 +69719,38 @@ async function action(options) {
 `);
   const payload = {
     created_at: new Date().toISOString(),
-    cerefox_version: process.env.npm_package_version ?? "unknown",
+    cerefox_version: PKG_VERSION,
+    backup_format: 4,
+    schema_version: schemaVersion,
     document_count: docs.length,
+    trashed_count: trashedCount,
+    includes_trash: includeTrash,
+    includes_lifecycle_status: lifecycleCaptured,
     chunk_count: chunkTotal,
+    project_count: projects.length,
+    membership_count: memberships.length,
+    relation_count: relations.length,
+    projects,
+    memberships,
+    relations,
     documents: enriched
   };
   writeFileSync(dest, JSON.stringify(payload, null, 2), "utf8");
   println("");
   println(c.green("✓ ") + `Backup written: ${dest}`);
-  println(c.dim(`  documents: ${docs.length} · chunks: ${chunkTotal}`));
+  println(c.dim(`  documents: ${docs.length} · chunks: ${chunkTotal} · ` + `projects: ${projects.length} · memberships: ${memberships.length}` + (relations.length > 0 ? ` · relations: ${relations.length}` : "")));
+  if (!includeTrash) {
+    println(c.dim("  trashed documents: excluded (--no-trash)"));
+  } else if (trashedCount > 0) {
+    println(c.dim(`  of which trashed: ${trashedCount} (restored as trash, not resurrected)`));
+  }
   if (options.git) {
     println(c.yellow("⚠ ") + "--git commit is not implemented; the snapshot was written without a git checkpoint.");
     println(c.dim("  Commit the backup directory yourself if you want it version-controlled."));
   }
 }
 function registerBackup(program2) {
-  program2.command("backup").description("Write a JSON snapshot of the knowledge base.").option("-o, --output-dir <dir>", "Snapshot output directory (default: CEREFOX_BACKUP_DIR or ~/.cerefox/backups).").option("-l, --label <label>", "Optional suffix added to the filename.").option("--include-versions", "Include archived versions in the snapshot. (v0.5: ignored — current chunks only.)").option("--git", "Commit the snapshot to the output dir as a git checkpoint. (v0.5: ignored.)").action(action);
+  program2.command("backup").description("Write a JSON snapshot of the knowledge base.").option("-o, --output-dir <dir>", "Snapshot output directory (default: CEREFOX_BACKUP_DIR or ~/.cerefox/backups).").option("-l, --label <label>", "Optional suffix added to the filename.").option("--include-versions", "Include archived versions in the snapshot. (v0.5: ignored — current chunks only.)").option("--git", "Commit the snapshot to the output dir as a git checkpoint. (v0.5: ignored.)").option("--no-trash", "Exclude soft-deleted documents. Default: they are captured and restored as trash.").action(action);
 }
 
 // src/cli/commands/completion.ts
@@ -69957,6 +70070,10 @@ var CONFIG_KEYS = [
     key: "min_term_coverage",
     description: "0–1 — fraction of a query's meaningful terms a keyword OR-fallback match must cover to count as confident. Default 0.5."
   },
+  {
+    key: "relations_enabled",
+    description: "'true'/'false' — expose the document-relation tools to agents. Off by default; the feature is dormant until enabled (iteration 29)."
+  },
   {
     key: "search_alpha",
     description: "0–1 — hybrid fusion weight: 1 = pure semantic, 0 = pure keyword. Default 0.7."
@@ -75502,8 +75619,8 @@ import { homedir as homedir6 } from "node:os";
 import { join as join9 } from "node:path";
 
 // ../../_shared/ef-meta/index.ts
-var EF_VERSION = "1.1.0-beta.1";
-var EF_LAST_CHANGED = "1.1.0-beta.1";
+var EF_VERSION = "1.1.0-beta.2";
+var EF_LAST_CHANGED = "1.1.0-beta.2";
 
 // src/cli/util/checks.ts
 init_config();
@@ -75852,7 +75969,7 @@ async function checkContentFormat() {
       name: CONTENT_FORMAT_CHECK_NAME,
       status: "skipped",
       detail: `${legacy} of ${total} document(s) use the legacy reconstruction format (format 1).`,
-      hint: "They auto-convert on next edit; run `cerefox server reindex` to convert all now. What this means: `cerefox guides show content-format`."
+      hint: "Harmless — they auto-convert on next edit. To convert them all now: `cerefox server migrate-format` (re-embeds, so try `--dry-run` first). To read what chunk formats are: `cerefox guides show content-format`."
     };
   } catch (err) {
     return {
@@ -77997,6 +78114,114 @@ function registerReindex(program2) {
   program2.command("reindex").description("Re-embed existing document chunks (v0.7+).").option("--all", "Reindex every chunk regardless of embedder.").option("--batch <n>", "Chunks per OpenAI batch call. Capped at 96 internally.", "32").option("--dry-run", "Show counts without re-embedding.").option("-i, --document-id <uuid>", "Limit reindex to a single document.").action(action27);
 }
 
+// src/cli/commands/migrate-format.ts
+init_cli_core();
+init_config();
+init_client();
+var CURRENT_FORMAT = 2;
+async function action28(options) {
+  const settings = loadSettings();
+  const client = getClient();
+  const supabase = client.raw;
+  let legacyChunkRows;
+  try {
+    legacyChunkRows = await fetchAllPages((from, to) => {
+      let q = supabase.from("cerefox_chunks").select("document_id").is("version_id", null).lt("content_format", CURRENT_FORMAT);
+      if (options.documentId)
+        q = q.eq("document_id", options.documentId);
+      return q.order("document_id", { ascending: true }).range(from, to);
+    }, 1000);
+  } catch (err) {
+    throw systemError(`Could not list legacy chunks: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  const docIds = [...new Set(legacyChunkRows.map((r) => r.document_id))];
+  const limit = options.limit ? parsePositiveInt(options.limit, "--limit", docIds.length) : docIds.length;
+  const targets = docIds.slice(0, limit);
+  if (targets.length === 0) {
+    println(c.green("✓ Nothing to migrate — every document already uses the current format."));
+    return;
+  }
+  println(c.bold(`${docIds.length} document(s) on the legacy format` + (targets.length < docIds.length ? `; converting ${targets.length} (--limit)` : "")));
+  if (options.dryRun) {
+    println(c.yellow("⚠  --dry-run: nothing was written."));
+    println(c.dim("   Each document would be re-chunked and RE-EMBEDDED (embedding spend)."));
+    return;
+  }
+  println(c.dim("Each document is re-chunked and re-embedded — this costs embedding spend."));
+  println("");
+  const author = resolveAuthor(options.author);
+  const authorType = resolveAuthorType(undefined);
+  const pipeline2 = new IngestionPipeline({
+    supabase,
+    openAiApiKey: settings.openaiApiKey
+  });
+  let converted = 0;
+  let skipped = 0;
+  const duplicates = [];
+  const failures = [];
+  for (let i = 0;i < targets.length; i++) {
+    const id = targets[i];
+    if (process.stdout.isTTY) {
+      process.stderr.write(`\r  Converting ${i + 1}/${targets.length}…`);
+    }
+    let doc2 = null;
+    try {
+      const rows = await client.rpc("cerefox_get_document", { p_document_id: id, p_version_id: null });
+      doc2 = rows?.[0] ?? null;
+    } catch (err) {
+      failures.push({ document: id, reason: `read: ${err instanceof Error ? err.message : String(err)}` });
+      continue;
+    }
+    if (!doc2) {
+      failures.push({ document: id, reason: "read: document not found" });
+      continue;
+    }
+    try {
+      await pipeline2.ingestText({
+        text: doc2.full_content,
+        title: doc2.doc_title,
+        documentId: id,
+        source: "migrate-format",
+        author,
+        authorType,
+        expectedContentHash: doc2.content_hash
+      });
+      converted++;
+    } catch (err) {
+      const message = err instanceof Error ? err.message : String(err);
+      if (/conflict/i.test(message)) {
+        skipped++;
+      } else if (/identical content already exists/i.test(message)) {
+        duplicates.push({ document: `${doc2.doc_title} (${id})`, reason: message });
+      } else {
+        failures.push({ document: `${doc2.doc_title} (${id})`, reason: message });
+      }
+    }
+  }
+  if (process.stdout.isTTY)
+    process.stderr.write(`
+`);
+  println("");
+  println(c.bold(`Converted ${converted} · skipped ${skipped} (changed mid-run) · failed ${failures.length}`));
+  if (targets.length < docIds.length) {
+    println(c.dim(`  ${docIds.length - targets.length} document(s) still pending — re-run to continue.`));
+  }
+  if (duplicates.length > 0) {
+    println("");
+    println(c.yellow(`⚠ ${duplicates.length} document(s) could not be converted because their content is ` + "byte-identical to another document."));
+    println(c.dim("  Re-ingesting them would collide with the content-hash dedup check. They keep working " + "on the legacy format; de-duplicate them if you want them converted."));
+    printTable(duplicates.map((d) => ({ document: d.document })));
+  }
+  if (failures.length > 0) {
+    println("");
+    printTable(failures);
+    throw systemError(`${failures.length} document(s) failed to convert.`);
+  }
+}
+function registerMigrateFormat(program2) {
+  program2.command("migrate-format").description("Convert legacy-format documents to the current chunk format (re-chunks + re-embeds).").option("--dry-run", "Report how many documents would be converted; write nothing.").option("-l, --limit <n>", "Convert at most N documents (re-run to continue).").option("--document-id <uuid>", "Convert a single document.").option("--author <name>", "Recorded in the audit log for each conversion.").action(action28);
+}
+
 // src/cli/commands/restore.ts
 init_cli_core();
 init_client();
@@ -78024,7 +78249,7 @@ function resolveBackupFile(target) {
   }
   return join12(path, candidates[0].name);
 }
-async function action28(target, options) {
+async function action29(target, options) {
   const file = resolveBackupFile(target);
   let payload;
   try {
@@ -78036,7 +78261,17 @@ async function action28(target, options) {
     throw userError(`Backup file is missing "documents" array: ${file}`);
   }
   println(c.bold(`Restoring from ${file}`));
-  println(c.dim(`  cerefox_version: ${payload.cerefox_version ?? "?"} · ` + `documents in file: ${payload.documents.length} · chunks in file: ${payload.chunk_count ?? "?"}`));
+  const hasMemberships = Array.isArray(payload.memberships);
+  println(c.dim(`  cerefox_version: ${payload.cerefox_version ?? "?"} · ` + `schema: ${payload.schema_version ?? "?"} · ` + `documents in file: ${payload.documents.length} · chunks in file: ${payload.chunk_count ?? "?"}`));
+  if (hasMemberships) {
+    println(c.dim(`  projects: ${payload.projects?.length ?? 0} · memberships: ${payload.memberships?.length ?? 0}`));
+  } else {
+    warn("This backup predates project-membership capture (format 1) — documents " + "will be restored WITHOUT their project assignments.");
+  }
+  const trashedInFile = payload.documents.filter((d) => d.deleted_at != null).length;
+  if (trashedInFile > 0) {
+    println(c.dim(`  trashed documents in file: ${trashedInFile} — restored as trash ` + "(still deleted; recover with `cerefox document restore`)"));
+  }
   println("");
   const client = getClient();
   let restored = 0;
@@ -78044,7 +78279,7 @@ async function action28(target, options) {
   let errors4 = 0;
   const errorDetails = [];
   for (const doc2 of payload.documents) {
-    const { data: existing } = await client.raw.from("cerefox_documents").select("id").eq("content_hash", doc2.content_hash).maybeSingle();
+    const { data: existing } = await client.raw.from("cerefox_documents").select("id").or(`id.eq.${doc2.id},content_hash.eq.${doc2.content_hash}`).limit(1).maybeSingle();
     if (existing) {
       skipped++;
       continue;
@@ -78071,8 +78306,70 @@ async function action28(target, options) {
     }
     restored++;
   }
+  let projectsRestored = 0;
+  let membershipsRestored = 0;
+  let relationsRestored = 0;
+  if (!options.dryRun && hasMemberships) {
+    const projects = payload.projects ?? [];
+    if (projects.length > 0) {
+      const { error: projErr } = await client.raw.from("cerefox_projects").upsert(projects, { onConflict: "id", ignoreDuplicates: true });
+      if (projErr) {
+        errors4++;
+        errorDetails.push({ title: "(projects)", error: projErr.message });
+      } else {
+        projectsRestored = projects.length;
+      }
+    }
+    const presentDocIds = new Set;
+    {
+      const ids = (payload.documents ?? []).map((d) => d.id);
+      for (let i = 0;i < ids.length; i += 200) {
+        const { data } = await client.raw.from("cerefox_documents").select("id").in("id", ids.slice(i, i + 200));
+        for (const row of data ?? [])
+          presentDocIds.add(row.id);
+      }
+    }
+    const links = (payload.memberships ?? []).filter((m) => presentDocIds.has(m.document_id));
+    for (let i = 0;i < links.length; i += 500) {
+      const { error: linkErr } = await client.raw.from("cerefox_document_projects").upsert(links.slice(i, i + 500), {
+        onConflict: "document_id,project_id",
+        ignoreDuplicates: true
+      });
+      if (linkErr) {
+        errors4++;
+        errorDetails.push({ title: "(memberships)", error: linkErr.message });
+        break;
+      }
+      membershipsRestored += links.slice(i, i + 500).length;
+    }
+    const relations = (payload.relations ?? []).filter((r) => presentDocIds.has(r.source_id) && presentDocIds.has(r.target_id));
+    if (relations.length > 0) {
+      for (let i = 0;i < relations.length; i += 500) {
+        const { error: relErr } = await client.raw.from("cerefox_document_relations").upsert(relations.slice(i, i + 500), {
+          onConflict: "source_id,target_id,rel_type",
+          ignoreDuplicates: true
+        });
+        if (relErr) {
+          errorDetails.push({ title: "(relations)", error: relErr.message });
+          errors4++;
+          break;
+        }
+        relationsRestored += relations.slice(i, i + 500).length;
+      }
+      const dropped = (payload.relations?.length ?? 0) - relations.length;
+      if (dropped > 0) {
+        warn(`${dropped} relation(s) skipped — one or both documents were not restored.`);
+      }
+    }
+  }
   println("");
   println((options.dryRun ? c.yellow("(dry-run) ") : "") + c.bold(`Summary: ${restored} restored · ${skipped} skipped · ${errors4} errors`));
+  if (hasMemberships && !options.dryRun) {
+    println(c.dim(`  projects: ${projectsRestored} · memberships: ${membershipsRestored}` + (relationsRestored > 0 ? ` · relations: ${relationsRestored}` : "")));
+  }
+  if (trashedInFile > 0) {
+    println(c.dim(`  ${trashedInFile} of those are trashed and stay trashed.`));
+  }
   if (errors4 > 0) {
     println("");
     printTable(errorDetails);
@@ -78080,7 +78377,7 @@ async function action28(target, options) {
   }
 }
 function registerRestore(program2) {
-  program2.command("restore").description("Restore a JSON-snapshot backup into the knowledge base.").argument("<snapshot>", "Backup file (or directory; most recent is picked) produced by `cerefox backup`.").option("--dry-run", "Print what would be restored without writing.").option("-p, --project-name <name>", "Reserved for future use; currently ignored (project memberships ride along with each doc's metadata).").action(action28);
+  program2.command("restore").description("Restore a JSON-snapshot backup into the knowledge base.").argument("<snapshot>", "Backup file (or directory; most recent is picked) produced by `cerefox backup`.").option("--dry-run", "Print what would be restored without writing.").option("-p, --project-name <name>", "Reserved for future use; currently ignored. Project memberships are restored from the backup itself (format 2+).").action(action29);
 }
 
 // src/cli/commands/search.ts
@@ -78105,7 +78402,7 @@ async function embedQuery(query) {
 }
 
 // src/cli/commands/search.ts
-async function action29(query, options) {
+async function action30(query, options) {
   if (!query || query.trim() === "") {
     throw userError("Empty query.");
   }
@@ -78271,7 +78568,7 @@ async function action29(query, options) {
   }
 }
 function registerSearch(program2) {
-  program2.command("search").description("Search the knowledge base (hybrid FTS + semantic).").argument("<query>", "Natural-language search query.").option("-c, --match-count <n>", "Maximum number of documents to return.", "5").option("-p, --project-name <name>", "Filter results to a specific project.").option("-f, --metadata-filter <json>", "JSON containment filter; only docs whose metadata contains ALL pairs are returned.").option("--mode <mode>", "Search mode: docs (default), hybrid, fts.", "docs").option("--alpha <float>", "Semantic weight 0..1 (default: CEREFOX_SEARCH_ALPHA; else 0.7).").option("--min-score <float>", "Minimum cosine similarity threshold (default: CEREFOX_MIN_SEARCH_SCORE; else 0.5, or 0.6 with the local embedder).").option("--min-term-coverage <float>", "OR-fallback keyword matches must cover at least this fraction of the query's meaningful terms to count as confident hits (default: CEREFOX_MIN_TERM_COVERAGE; else the server default 0.5; needs schema ≥ 0.9.1).").option("--max-bytes <n>", "Response size budget in bytes (default: CEREFOX_MAX_RESPONSE_BYTES or 200000).").option("-r, --requestor <name>", "Agent / user name (recorded in usage log).").option("--json", "Emit machine-readable JSON instead of the default text.").option("--only-metadata", "List matching docs (id, score, chunks, chars, partial/full) WITHOUT their content — like the web UI's collapsed result list. Grab a [id:…] then `cerefox document get <id>`.").action(action29);
+  program2.command("search").description("Search the knowledge base (hybrid FTS + semantic).").argument("<query>", "Natural-language search query.").option("-c, --match-count <n>", "Maximum number of documents to return.", "5").option("-p, --project-name <name>", "Filter results to a specific project.").option("-f, --metadata-filter <json>", "JSON containment filter; only docs whose metadata contains ALL pairs are returned.").option("--mode <mode>", "Search mode: docs (default), hybrid, fts.", "docs").option("--alpha <float>", "Semantic weight 0..1 (default: CEREFOX_SEARCH_ALPHA; else 0.7).").option("--min-score <float>", "Minimum cosine similarity threshold (default: CEREFOX_MIN_SEARCH_SCORE; else 0.5, or 0.6 with the local embedder).").option("--min-term-coverage <float>", "OR-fallback keyword matches must cover at least this fraction of the query's meaningful terms to count as confident hits (default: CEREFOX_MIN_TERM_COVERAGE; else the server default 0.5; needs schema ≥ 0.9.1).").option("--max-bytes <n>", "Response size budget in bytes (default: CEREFOX_MAX_RESPONSE_BYTES or 200000).").option("-r, --requestor <name>", "Agent / user name (recorded in usage log).").option("--json", "Emit machine-readable JSON instead of the default text.").option("--only-metadata", "List matching docs (id, score, chunks, chars, partial/full) WITHOUT their content — like the web UI's collapsed result list. Grab a [id:…] then `cerefox document get <id>`.").action(action30);
 }
 
 // src/cli/commands/self-update.ts
@@ -78318,7 +78615,7 @@ async function fetchLatestVersion() {
   }
   return body.version;
 }
-async function action30(options) {
+async function action31(options) {
   let target;
   try {
     target = options.version ?? await fetchLatestVersion();
@@ -78371,7 +78668,7 @@ async function action30(options) {
 }
 function registerSelfUpdate(program2) {
   const desc = "Upgrade Cerefox in place. Alias: `cerefox upgrade`.";
-  const declaration = (cmd) => cmd.description(desc).option("--check", "Print current vs latest; do nothing.").option("--yes", "Non-interactive (skip confirmation).").option("--version <version>", "Pin a specific version (e.g. 0.5.1 or 0.6.0-rc.1).").action(action30);
+  const declaration = (cmd) => cmd.description(desc).option("--check", "Print current vs latest; do nothing.").option("--yes", "Non-interactive (skip confirmation).").option("--version <version>", "Pin a specific version (e.g. 0.5.1 or 0.6.0-rc.1).").action(action31);
   declaration(program2.command("self-update"));
   declaration(program2.command("upgrade"));
 }
@@ -78390,7 +78687,7 @@ function symbol2(status) {
       return cErr.dim("ℹ");
   }
 }
-async function action31(options) {
+async function action32(options) {
   const useSpinner = !options.json && process.stderr.isTTY;
   const spinner = useSpinner ? ora({ text: "Starting checks…", spinner: "dots", stream: process.stderr }).start() : null;
   const results = await runFastChecks({
@@ -78411,7 +78708,7 @@ async function action31(options) {
   }
 }
 function registerStatus(program2) {
-  program2.command("status").description("Quick sanity check (fast subset of `cerefox doctor`).").option("--json", "Emit machine-readable JSON.").action(action31);
+  program2.command("status").description("Quick sanity check (fast subset of `cerefox doctor`).").option("--json", "Emit machine-readable JSON.").action(action32);
 }
 
 // src/cli/commands/token.ts
@@ -78444,10 +78741,10 @@ function upsertEnvVar(path, key, value, opts = {}) {
   }
   const re = new RegExp(`^(\\s*)${escapeRegExp(key)}=.*$`, "m");
   let next;
-  let action32;
+  let action33;
   if (re.test(original)) {
     next = original.replace(re, `$1${line}`);
-    action32 = "updated";
+    action33 = "updated";
   } else {
     const base = original.endsWith(`
 `) ? original : `${original}
@@ -78455,10 +78752,10 @@ function upsertEnvVar(path, key, value, opts = {}) {
     next = `${base}
 ${header}${line}
 `;
-    action32 = "added";
+    action33 = "added";
   }
   writeFileSync5(path, next);
-  return { path, action: action32, backupPath };
+  return { path, action: action33, backupPath };
 }
 function readEnvVar(path, key) {
   if (!existsSync14(path))
@@ -83707,7 +84004,13 @@ import {
 } from "node:fs";
 import { homedir as homedir9 } from "node:os";
 import { join as join18 } from "node:path";
-var STATE_DIR = join18(homedir9(), ".cerefox");
+function resolveStateDir(override = process.env.CEREFOX_CONFIG_DIR, home = homedir9()) {
+  override = (override ?? "").trim();
+  if (!override)
+    return join18(home, ".cerefox");
+  return override === "~" || override.startsWith("~/") ? join18(home, override.slice(2)) : override;
+}
+var STATE_DIR = resolveStateDir();
 var PID_FILE = join18(STATE_DIR, "web.pid");
 var LOG_FILE = join18(STATE_DIR, "web.log");
 var daemonPaths = { stateDir: STATE_DIR, pidFile: PID_FILE, logFile: LOG_FILE };
@@ -84075,6 +84378,7 @@ Learn more:
   const server = program2.command("server").description("Server side: deploy, reindex.");
   moveInto(server, registerDeployServer, "deploy");
   moveInto(server, registerReindex, "reindex");
+  registerMigrateFormat(server);
   const guides = program2.command("guides").description("Bundled docs: list, open, show, ingest (into the KB).");
   registerGuides(guides);
   moveInto(guides, registerSyncSelfDocs, "ingest");