@gmickel/gno 2.10.0 → 2.10.1

package/README.md

@@ -139,7 +139,7 @@ See the [guide](docs/COMPILED-CONTEXT.md).
 
 <!-- public-truth:current-version -->
 
-> Current source version: **v2.10.0**. See [CHANGELOG.md](./CHANGELOG.md).
+> Current source version: **v2.10.1**. See [CHANGELOG.md](./CHANGELOG.md).
 
 <!-- /public-truth -->
 

package/browser-extension/artifacts/gno-browser-clipper-v2.10.1.zip.sha256

@@ -0,0 +1 @@
+e42897b28d0fc0fca7d1d7aca6ab016255cc3b5bf20d38bcac51535499eb7f25  gno-browser-clipper-v2.10.1.zip

package/browser-extension/dist/manifest.json

@@ -21,5 +21,5 @@
   "content_security_policy": {
     "extension_pages": "script-src 'self'; object-src 'none'; connect-src http://127.0.0.1:*"
   },
-  "version": "2.10.0"
+  "version": "2.10.1"
 }

package/bunfig.toml

@@ -2,6 +2,10 @@
 plugins = ["bun-plugin-tailwind"]
 
 [test]
-preload = ["./test/preload/happy-dom.ts", "./test/preload/env-guard.ts"]
+preload = [
+  "./test/preload/temp-dir.ts",
+  "./test/preload/happy-dom.ts",
+  "./test/preload/env-guard.ts",
+]
 # Frozen evidence and local experiments are not the executable regression suite.
 pathIgnorePatterns = [".flow/artifacts/**", "notes/**"]

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmickel/gno",
-  "version": "2.10.0",
+  "version": "2.10.1",
   "description": "Local semantic search for your documents. Index Markdown, PDF, and Office files with hybrid BM25 + vector search.",
   "keywords": [
     "embeddings",
@@ -72,6 +72,7 @@
     "test:e2e:install": "bunx playwright install chromium",
     "test:package": "bun scripts/package-smoke.ts",
     "test:package:clipper": "bun scripts/package-smoke-clipper-cli.ts",
+    "test:tmp-check": "bun scripts/test-tmp-check.ts",
     "test:watch": "bun test --watch",
     "test:coverage": "bun test --coverage",
     "test:coverage:html": "bun test --coverage --html",

package/spec/cli.md

@@ -242,8 +242,10 @@ the model with `id`, `model`, `dimensions`, `state` (`active`|`shadow`),
 Terminal output prints a `Vector partitions:` block
 unless there is exactly one healthy partition. `collections`, `totalDocuments`
 and `totalChunks` cover configured collections only: a collection removed from
-config (for example by `gno collection remove`) is not reported even while its
-rows remain in the index until the next `gno update`. `totalChunks` counts the
+config is not reported even while its rows remain in the index until the next
+command that syncs collections (`gno update`, `gno index`, `gno cleanup`). The
+embedding backlog likewise counts chunks of configured collections only.
+`gno collection remove` syncs at once, so no rows remain. `totalChunks` counts the
 distinct chunks of active documents; chunks left by deleted documents do not
 count. Per-collection chunk totals remain deduplicated by canonical chunk;
 embedded counts require matching current inputs for every active owner within
@@ -1097,12 +1099,12 @@ for `updateCmd`; without it the command is stopped after 10 minutes.
 
 ### gno collection remove
 
-Remove a collection from the index.
+Remove a collection from the config and the index.
 
 **Synopsis:**
 
 ```bash
-gno collection remove <name>
+gno collection remove <name> [--lock-wait <duration>] [--no-wait]
 ```
 
 **Arguments:**
@@ -1113,12 +1115,19 @@ gno collection remove <name>
 **Behavior:**
 
 - Removes collection from config
-- Marks documents as inactive (does not delete DB rows until `cleanup`)
+- Syncs the index in the same config write: the collection row and its
+  documents are deleted at once, so status, search and the embedding backlog
+  stop counting them without another command
+- Content, chunks and vectors no longer referenced by any document stay until
+  `gno cleanup`
+- Waits for the index write lease (`--lock-wait`, default 120s; `--no-wait`
+  fails at once)
 
 **Exit Codes:**
 
 - 0: Success
-- 1: Collection not found
+- 1: Collection not found or referenced by contexts
+- 2: Config save or index sync failure, or write lease busy
 
 ---
 
@@ -1129,7 +1138,7 @@ Rename a collection.
 **Synopsis:**
 
 ```bash
-gno collection rename <old> <new>
+gno collection rename <old> <new> [--lock-wait <duration>] [--no-wait]
 ```
 
 **Arguments:**
@@ -1138,10 +1147,22 @@ gno collection rename <old> <new>
 | `<old>` | string | Current collection name |
 | `<new>` | string | New collection name |
 
+**Behavior:**
+
+- Renames the collection in config and rewrites contexts scoped to it
+- Syncs the index in the same config write. Documents are keyed by collection
+  name, so the old name's documents are deleted at once and the collection is
+  empty until the next `gno update` (or `gno index`) indexes its files under
+  the new name; content and vectors not yet removed by `gno cleanup` are reused
+- Prints `Run: gno update to index it under the new name`
+- Waits for the index write lease (`--lock-wait`, default 120s; `--no-wait`
+  fails at once)
+
 **Exit Codes:**
 
 - 0: Success
-- 1: Old name not found or new name already exists
+- 1: Old name not found, new name already exists, or new name invalid
+- 2: Config save or index sync failure, or write lease busy
 
 ---
 
@@ -2944,12 +2965,13 @@ included, is refused. JSON output is
 
 ### gno cleanup
 
-Remove orphaned content, chunks, and vectors not referenced by active documents.
+Remove documents of collections no longer in the config, then orphaned
+content, chunks, and vectors not referenced by active documents.
 
 **Synopsis:**
 
 ```bash
-gno cleanup
+gno cleanup [--lock-wait <duration>] [--no-wait]
 ```
 
 **Exit Codes:**

package/spec/mcp.md

@@ -2830,7 +2830,7 @@ Full index: sync files + generate embeddings (write-enabled). Runs as background
 
 ### gno_remove_collection
 
-Remove a collection from config (write-enabled). Indexed data is retained.
+Remove a collection from config and delete its documents from the index (write-enabled). Content, chunks and vectors stay until `gno cleanup`; `indexedDataRetained` is always `true` for that reason.
 
 **Input Schema:**
 

package/spec/output-schemas/mcp-remove-result.schema.json

@@ -28,12 +28,12 @@
     },
     "indexedDataRetained": {
       "type": "boolean",
-      "description": "Indexed data retention flag",
+      "description": "Always true: the collection's documents are deleted, but content, chunks and vectors stay in the index until gno cleanup",
       "const": true
     },
     "note": {
       "type": "string",
-      "description": "Explanation of retained data"
+      "description": "What was deleted and what stays until gno cleanup"
     }
   }
 }

package/src/cli/commands/cleanup.ts

@@ -1,6 +1,7 @@
 /**
  * gno cleanup command implementation.
- * Remove orphaned content, chunks, vectors not referenced by active documents.
+ * Remove documents of collections no longer configured, then orphaned
+ * content, chunks and vectors not referenced by active documents.
  *
  * @module src/cli/commands/cleanup
  */
@@ -61,6 +62,13 @@ export async function cleanup(
   }
 
   try {
+    // Drop collections no longer in the config first (their documents follow
+    // by cascade), so their content, chunks and vectors count as orphans.
+    const syncResult = await store.syncCollections(config.collections);
+    if (!syncResult.ok) {
+      return { success: false, error: syncResult.error.message };
+    }
+
     const cleanupResult = await store.cleanupOrphans();
     if (!cleanupResult.ok) {
       return { success: false, error: cleanupResult.error.message };

package/src/cli/commands/collection/remove.ts

@@ -3,43 +3,62 @@
  */
 
 import { removeCollection } from "../../../collection";
-import { applyConfigFileChange } from "../../../core/config-mutation";
+import { applyConfigChange } from "../../../core/config-mutation";
 import { CliError } from "../../errors";
+import { initStore } from "../shared";
 
 export async function collectionRemove(
   name: string,
-  options: { configPath?: string } = {}
+  options: { configPath?: string; indexName?: string } = {}
 ): Promise<void> {
-  const mutation = await applyConfigFileChange(
-    { configPath: options.configPath },
-    (config) => {
-      const result = removeCollection(config, { name });
-      return result.ok
-        ? {
-            ok: true as const,
-            config: result.config,
-            value: result.collection,
-          }
-        : {
-            ok: false as const,
-            error: result.message,
-            code: result.code,
-          };
+  // Open the index so the removal reaches the store in the same locked
+  // boundary: syncing collections deletes the collection row, and its
+  // documents follow by cascade. A config-only edit left them active (and
+  // counted in the embedding backlog) until some later command synced.
+  const initialized = await initStore({
+    configPath: options.configPath,
+    indexName: options.indexName,
+    syncConfig: false,
+    allowEmptyCollections: true,
+  });
+  if (!initialized.ok) {
+    throw new CliError("RUNTIME", initialized.error);
+  }
+
+  try {
+    const mutation = await applyConfigChange(
+      { store: initialized.store, configPath: initialized.actualConfigPath },
+      (config) => {
+        const result = removeCollection(config, { name });
+        return result.ok
+          ? {
+              ok: true as const,
+              config: result.config,
+              value: result.collection,
+            }
+          : {
+              ok: false as const,
+              error: result.message,
+              code: result.code,
+            };
+      }
+    );
+
+    if (!mutation.ok) {
+      // Map collection error codes to CLI error codes
+      const cliCode =
+        mutation.code === "VALIDATION" ||
+        mutation.code === "NOT_FOUND" ||
+        mutation.code === "HAS_REFERENCES"
+          ? "VALIDATION"
+          : "RUNTIME";
+      throw new CliError(cliCode, mutation.error);
     }
-  );
 
-  if (!mutation.ok) {
-    // Map collection error codes to CLI error codes
-    const cliCode =
-      mutation.code === "VALIDATION" ||
-      mutation.code === "NOT_FOUND" ||
-      mutation.code === "HAS_REFERENCES"
-        ? "VALIDATION"
-        : "RUNTIME";
-    throw new CliError(cliCode, mutation.error);
+    process.stdout.write(
+      `Collection "${mutation.value?.name}" removed successfully\n`
+    );
+  } finally {
+    await initialized.store.close();
   }
-
-  process.stdout.write(
-    `Collection "${mutation.value?.name}" removed successfully\n`
-  );
 }

package/src/cli/commands/collection/rename.ts

@@ -3,19 +3,51 @@
  */
 
 import { CollectionSchema, getCollectionFromScope } from "../../../config";
-import { applyConfigFileChange } from "../../../core/config-mutation";
+import { applyConfigChange } from "../../../core/config-mutation";
 import { CliError } from "../../errors";
+import { initStore, type InitStoreResult } from "../shared";
 
 export async function collectionRename(
   oldName: string,
   newName: string,
-  options: { configPath?: string } = {}
+  options: { configPath?: string; indexName?: string } = {}
 ): Promise<void> {
   const oldCollectionName = oldName.toLowerCase();
   const newCollectionName = newName.toLowerCase();
 
-  const mutation = await applyConfigFileChange(
-    { configPath: options.configPath },
+  // Documents are keyed by collection name (URIs, FTS paths, links), so the
+  // index cannot rename them in place. Sync in the same locked boundary: the
+  // old name's documents go now instead of at some later sync, and the next
+  // update indexes the files under the new name.
+  const initialized = await initStore({
+    configPath: options.configPath,
+    indexName: options.indexName,
+    syncConfig: false,
+    allowEmptyCollections: true,
+  });
+  if (!initialized.ok) {
+    throw new CliError("RUNTIME", initialized.error);
+  }
+
+  try {
+    await renameAndSync(initialized, oldCollectionName, newCollectionName);
+  } finally {
+    await initialized.store.close();
+  }
+
+  process.stdout.write(
+    `Collection "${oldCollectionName}" renamed to "${newCollectionName}"\n` +
+      "Run: gno update to index it under the new name\n"
+  );
+}
+
+async function renameAndSync(
+  initialized: Extract<InitStoreResult, { ok: true }>,
+  oldCollectionName: string,
+  newCollectionName: string
+): Promise<void> {
+  const mutation = await applyConfigChange(
+    { store: initialized.store, configPath: initialized.actualConfigPath },
     (config) => {
       const collection = config.collections.find(
         (item) => item.name === oldCollectionName
@@ -70,8 +102,4 @@ export async function collectionRename(
       mutation.error
     );
   }
-
-  process.stdout.write(
-    `Collection "${oldCollectionName}" renamed to "${newCollectionName}"\n`
-  );
 }

package/src/cli/program.ts

@@ -2870,23 +2870,59 @@ function wireManagementCommands(program: Command): void {
       });
     });
 
-  collectionCmd
-    .command("remove <name>")
-    .description("Remove a collection")
-    .action(async (name: string) => {
-      const { collectionRemove } = await import("./commands/collection");
-      await collectionRemove(name, { configPath: getGlobals().config });
-    });
+  addWriteLeaseFlags(
+    collectionCmd
+      .command("remove <name>")
+      .description("Remove a collection and its indexed documents")
+  ).action(async (name: string, cmdOpts: Record<string, unknown>) => {
+    const { collectionRemove } = await import("./commands/collection");
+    const lease = parseWriteLeaseFlags(cmdOpts);
+    const result = await withCliWriteLease(
+      {
+        indexName: getGlobals().index,
+        lockWaitMs: lease.lockWaitMs,
+        noWait: lease.noWait,
+      },
+      async () => {
+        await collectionRemove(name, {
+          configPath: getGlobals().config,
+          indexName: getGlobals().index,
+        });
+        return { success: true as const };
+      }
+    );
+    throwIfWriteLeaseBusy(result, false);
+  });
 
-  collectionCmd
-    .command("rename <old> <new>")
-    .description("Rename a collection")
-    .action(async (oldName: string, newName: string) => {
+  addWriteLeaseFlags(
+    collectionCmd
+      .command("rename <old> <new>")
+      .description("Rename a collection (run gno update afterwards)")
+  ).action(
+    async (
+      oldName: string,
+      newName: string,
+      cmdOpts: Record<string, unknown>
+    ) => {
       const { collectionRename } = await import("./commands/collection");
-      await collectionRename(oldName, newName, {
-        configPath: getGlobals().config,
-      });
-    });
+      const lease = parseWriteLeaseFlags(cmdOpts);
+      const result = await withCliWriteLease(
+        {
+          indexName: getGlobals().index,
+          lockWaitMs: lease.lockWaitMs,
+          noWait: lease.noWait,
+        },
+        async () => {
+          await collectionRename(oldName, newName, {
+            configPath: getGlobals().config,
+            indexName: getGlobals().index,
+          });
+          return { success: true as const };
+        }
+      );
+      throwIfWriteLeaseBusy(result, false);
+    }
+  );
 
   addWriteLeaseFlags(
     collectionCmd
@@ -3620,7 +3656,11 @@ function wireManagementCommands(program: Command): void {
         lockWaitMs: lease.lockWaitMs,
         noWait: lease.noWait,
       },
-      () => cleanup({ indexName: getGlobals().index })
+      () =>
+        cleanup({
+          configPath: getGlobals().config,
+          indexName: getGlobals().index,
+        })
     );
     throwIfWriteLeaseBusy(result, false);
 

package/src/mcp/tools/remove-collection.ts

@@ -21,6 +21,7 @@ interface RemoveCollectionResult {
   removed: true;
   collection: string;
   configUpdated: true;
+  /** Documents are deleted; content, chunks and vectors stay until cleanup. */
   indexedDataRetained: true;
   note: string;
 }
@@ -101,7 +102,7 @@ export function handleRemoveCollection(
           collection: name,
           configUpdated: true,
           indexedDataRetained: true,
-          note: "Documents remain in index until next full reindex or manual cleanup",
+          note: "Collection removed from config and its documents deleted from the index. Content, chunks and vectors stay until gno cleanup.",
         };
 
         return result;

package/src/serve/routes/api.ts

@@ -1574,9 +1574,8 @@ export async function handleImportPreview(
 
 /**
  * DELETE /api/collections/:name
- * Remove a collection from config.
- * Note: Does NOT remove indexed documents - they remain in DB until re-sync
- * or manual cleanup. This preserves data for potential recovery.
+ * Remove a collection from config. The config sync deletes the collection
+ * row and its documents; content, chunks and vectors stay until cleanup.
  */
 export async function handleDeleteCollection(
   ctxHolder: ContextHolder,
@@ -1612,7 +1611,7 @@ export async function handleDeleteCollection(
   return jsonResponse({
     success: true,
     collection: name,
-    note: "Collection removed from config. Indexed documents remain in DB.",
+    note: "Collection removed from config and its documents deleted from the index. Content, chunks and vectors stay until gno cleanup.",
   });
 }
 

package/src/store/sqlite/adapter.ts

@@ -6124,18 +6124,25 @@ export class SqliteAdapter implements StorePort, SqliteDbProvider {
           )
           .get(configuredJson, configuredJson)?.count ?? 0;
 
-      // Embedding backlog: chunks from active docs without vectors
-      // Uses EXISTS to avoid duplicates when multiple docs share mirror_hash
+      // Embedding backlog: chunks from active docs of configured collections
+      // without vectors. DISTINCT avoids duplicates when docs share mirror_hash.
       const backlogRow = db
         .query<
           { count: number },
-          [string | null, string | null, string | null]
+          [
+            string | null,
+            string | null,
+            string | null,
+            string | null,
+            string | null,
+          ]
         >(
           `
           WITH active_mirrors AS (
             SELECT DISTINCT mirror_hash
             FROM documents
             WHERE active = 1 AND mirror_hash IS NOT NULL
+              AND (? IS NULL OR collection IN (SELECT value FROM json_each(?)))
           ),
           matching_vectors AS (
             SELECT mirror_hash, seq, MAX(embedded_at) AS embedded_at
@@ -6155,7 +6162,13 @@ export class SqliteAdapter implements StorePort, SqliteDbProvider {
           WHERE mv.mirror_hash IS NULL
         `
         )
-        .get(embedModel, embedModel, embedFingerprint);
+        .get(
+          configuredJson,
+          configuredJson,
+          embedModel,
+          embedModel,
+          embedFingerprint
+        );
 
       // Recent errors (last 24h)
       const recentErrorsRow = db

package/browser-extension/artifacts/gno-browser-clipper-v2.10.0.zip.sha256

@@ -1 +0,0 @@
-56174f38783259cef05d81ae53adceebc8467799b735c2f3026b928f7070ae76  gno-browser-clipper-v2.10.0.zip