gnosys 5.4.0 → 5.4.1

package/README.md

@@ -24,7 +24,7 @@
 
 Gnosys is **sandbox-first**: a persistent background process holds the database connection while agents import a tiny helper library and call memory operations like normal code — no MCP schemas, no round-trips, near-zero context cost. The central brain at `~/.gnosys/gnosys.db` unifies all projects, user preferences, and global knowledge. Federated search ranks results across scopes with tier boosting and recency awareness. The **Web Knowledge Base** turns any website into a searchable knowledge base for serverless chatbots — pre-computed JSON index, zero runtime dependencies. **Multimodal ingestion** handles PDFs, images, audio, and video. **Portfolio Dashboard** gives a bird's-eye view of all projects. Process tracing builds call chains from source code. Dream Mode consolidates knowledge during idle time. One-command export regenerates a full Obsidian vault.
 
-It also runs as a CLI and a complete MCP server that drops straight into Cursor, Claude Desktop, Claude Code, Cowork, Codex, or any MCP client.
+It also runs as a CLI and a complete MCP server that drops straight into Cursor, Claude Desktop (Chat / Cowork / Code), Claude Code, Codex, Gemini CLI, Antigravity, or any MCP client.
 
 No vector DBs. No black boxes. No external services. Just SQLite and optional Obsidian export — the way knowledge should be.
 
@@ -53,7 +53,7 @@ Gnosys takes a different approach: the central brain is a single SQLite database
 - **Bulk import** — CSV, JSON, JSONL. Import entire datasets in seconds.
 - **Obsidian-native** — `gnosys export` generates a full vault with YAML frontmatter, `[[wikilinks]]`, summaries, and graph data.
 - **Multi-machine sync (v5.3.0)** — share your `gnosys.db` across machines via NAS or shared drive. Local cache for speed, remote source of truth for consistency. Built-in conflict detection with skip-and-flag resolution. Run `gnosys remote configure` to set up.
-- **MCP-compatible** — also runs as a full MCP server that drops into Cursor, Claude Desktop, Claude Code, Cowork, Codex, or any MCP client.
+- **MCP-compatible** — also runs as a full MCP server that drops into Cursor, Claude Desktop (Chat / Cowork / Code), Claude Code, Codex, Gemini CLI, Antigravity, or any MCP client.
 - **Zero infrastructure** — no external databases, no Docker (unless you want it), no cloud services. Just `npm install`.
 
 > For the complete CLI reference and detailed guides, see the **[User Guide](https://gnosys.ai/guide.html)**.
@@ -235,9 +235,47 @@ This improves your site's visibility in AI-powered search results and enables LL
 
 ## MCP Server Setup
 
-### Claude Desktop
+The fastest way to wire gnosys into any supported client is to run `gnosys init <ide>` from the project directory you want memory-enabled. Examples:
 
-Add to `~/Library/Application Support/Claude/claude_desktop_config.json`:
+```bash
+gnosys init claude-desktop   # Claude Desktop (covers Chat, Cowork, and Code)
+gnosys init claude           # Claude Code CLI
+gnosys init cursor           # Cursor
+gnosys init codex            # Codex
+gnosys init gemini-cli       # Gemini CLI
+gnosys init antigravity      # Google Antigravity
+```
+
+This does two things at once:
+1. Wires gnosys into the IDE's MCP config (idempotent — safe to re-run).
+2. Initializes the current directory as a gnosys project (creates `.gnosys/gnosys.json`, registers it in the central DB) so your memories can be scoped to it.
+
+### One-time vs. per-project
+
+The IDE wiring writes to a **user-level** config file, so it only needs to happen **once**. Re-running it in another project just re-merges the same `mcpServers.gnosys` entry — harmless.
+
+The project registration is **per-directory**: every codebase you want to be memory-aware of needs its own `gnosys init`. From then on, agents pass `projectRoot: "/path/to/project"` to gnosys MCP tools to scope memory to that codebase.
+
+```bash
+# Once, anywhere — wires Claude Desktop's MCP config:
+gnosys init claude-desktop
+
+# Once per project — registers the codebase in the central DB:
+cd /path/to/project-a && gnosys init
+cd /path/to/project-b && gnosys init
+```
+
+> **Cowork users:** Cowork sessions don't have a working directory like a CLI does. The agent in Cowork uses whichever `projectRoot` it's told to use (typically auto-detected from open files or set via the system prompt). The "every working directory" question doesn't apply to Cowork itself — only to the projects you want memory-enabled. Run `gnosys init claude-desktop` once globally; run `gnosys init` per project.
+
+---
+
+### Manual config (if you prefer)
+
+If you'd rather edit configs by hand, here's where each client looks for MCP servers.
+
+#### Claude Desktop (Chat, Cowork, and Code share the same config)
+
+Add to `~/Library/Application Support/Claude/claude_desktop_config.json` (macOS), `%APPDATA%\Claude\claude_desktop_config.json` (Windows), or `~/.config/Claude/claude_desktop_config.json` (Linux):
 
 ```json
 {
@@ -250,9 +288,11 @@ Add to `~/Library/Application Support/Claude/claude_desktop_config.json`:
 }
 ```
 
-### Cursor
+Restart Claude Desktop after editing.
+
+#### Cursor
 
-Add to `.cursor/mcp.json`:
+Add to `.cursor/mcp.json` in your project:
 
 ```json
 {
@@ -265,13 +305,13 @@ Add to `.cursor/mcp.json`:
 }
 ```
 
-### Claude Code
+#### Claude Code
 
 ```bash
 claude mcp add gnosys gnosys serve
 ```
 
-### Codex
+#### Codex
 
 Add to `.codex/config.toml`:
 
@@ -281,6 +321,38 @@ type = "local"
 command = ["gnosys", "serve"]
 ```
 
+#### Gemini CLI
+
+Add to `~/.gemini/settings.json` (preserves any existing settings):
+
+```json
+{
+  "mcpServers": {
+    "gnosys": {
+      "command": "gnosys",
+      "args": ["serve"]
+    }
+  }
+}
+```
+
+#### Antigravity
+
+Add to `~/.gemini/antigravity/mcp_config.json`:
+
+```json
+{
+  "mcpServers": {
+    "gnosys": {
+      "command": "gnosys",
+      "args": ["serve"]
+    }
+  }
+}
+```
+
+Antigravity reloads MCP servers automatically when you save the file.
+
 > **Note:** API keys are configured via `gnosys setup` (macOS Keychain, environment variable, or `~/.config/gnosys/.env`). See [LLM Provider Setup](https://gnosys.ai/guide.html#guide-llm-provider-setup) in the User Guide.
 
 ---

package/dist/cli.js

@@ -507,7 +507,8 @@ setupCmd
     .option("--path <path>", "Set remote path directly (non-interactive)")
     .action(async (opts) => {
     const { GnosysDB } = await import("./lib/db.js");
-    const db = GnosysDB.openCentral();
+    // Sync configuration needs explicit local DB access (not auto-routed remote).
+    const db = GnosysDB.openLocal();
     if (!db.isAvailable()) {
         console.error("Central DB not available.");
         db.close();
@@ -1713,14 +1714,60 @@ program
     .command("graph")
     .description("Show the full cross-reference graph across all memories")
     .action(async () => {
-    const resolver = await getResolver();
-    const allMemories = await resolver.getAllMemories();
-    if (allMemories.length === 0) {
-        console.log("No memories found.");
-        return;
+    // v5.4.1: Query the central DB directly. Previously this used the
+    // filesystem resolver, which returns nothing in v5.x DB-only mode
+    // because memories no longer live as markdown files.
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        if (!centralDb.isAvailable()) {
+            console.error("Central DB not available.");
+            process.exit(1);
+        }
+        const dbMemories = centralDb.getAllMemories();
+        if (dbMemories.length === 0) {
+            console.log("No memories found.");
+            return;
+        }
+        // Adapt DbMemory → legacy Memory shape that buildLinkGraph expects.
+        // The graph builder only reads id, title, content, and synthesises
+        // a filesystem-style path for display.
+        const adapted = dbMemories.map((m) => {
+            let parsedTags = [];
+            try {
+                parsedTags = JSON.parse(m.tags);
+            }
+            catch {
+                parsedTags = [];
+            }
+            const relativePath = `${m.category}/${m.id}.md`;
+            return {
+                frontmatter: {
+                    id: m.id,
+                    title: m.title,
+                    category: m.category,
+                    tags: parsedTags,
+                    relevance: m.relevance,
+                    author: m.author,
+                    authority: m.authority,
+                    confidence: m.confidence,
+                    created: m.created,
+                    modified: m.modified,
+                    last_reviewed: m.modified,
+                    status: m.status,
+                    supersedes: m.supersedes,
+                },
+                content: m.content,
+                filePath: relativePath,
+                relativePath,
+            };
+        });
+        const graph = buildLinkGraph(adapted);
+        console.log(formatGraphSummary(graph));
+    }
+    finally {
+        centralDb?.close();
     }
-    const graph = buildLinkGraph(allMemories);
-    console.log(formatGraphSummary(graph));
 });
 // ─── gnosys bootstrap <sourceDir> ────────────────────────────────────────
 program
@@ -2541,7 +2588,8 @@ remoteCmd
     .action(async (opts) => {
     let centralDb = null;
     try {
-        centralDb = GnosysDB.openCentral();
+        // Sync operations need explicit local DB access (not auto-routed remote).
+        centralDb = GnosysDB.openLocal();
         if (!centralDb.isAvailable()) {
             console.error("Central DB not available.");
             process.exit(1);
@@ -2592,7 +2640,7 @@ remoteCmd
     .action(async (opts) => {
     let centralDb = null;
     try {
-        centralDb = GnosysDB.openCentral();
+        centralDb = GnosysDB.openLocal();
         if (!centralDb.isAvailable()) {
             console.error("Central DB not available.");
             process.exit(1);
@@ -2606,7 +2654,8 @@ remoteCmd
         const sync = new RemoteSync(centralDb, remotePath);
         const result = await sync.push({ strategy: opts.newerWins ? "newer-wins" : "skip-and-flag" });
         sync.closeRemote();
-        console.log(`Pushed: ${result.pushed} | Skipped: ${result.skipped} | Conflicts: ${result.conflicts.length}`);
+        const projParts = (result.projectsPushed || 0) > 0 ? ` | Projects pushed: ${result.projectsPushed}` : "";
+        console.log(`Pushed: ${result.pushed} | Skipped: ${result.skipped} | Conflicts: ${result.conflicts.length}${projParts}`);
         if (result.errors.length > 0) {
             console.log("\nErrors:");
             for (const e of result.errors)
@@ -2633,7 +2682,7 @@ remoteCmd
     .action(async (opts) => {
     let centralDb = null;
     try {
-        centralDb = GnosysDB.openCentral();
+        centralDb = GnosysDB.openLocal();
         if (!centralDb.isAvailable()) {
             console.error("Central DB not available.");
             process.exit(1);
@@ -2647,7 +2696,8 @@ remoteCmd
         const sync = new RemoteSync(centralDb, remotePath);
         const result = await sync.pull({ strategy: opts.newerWins ? "newer-wins" : "skip-and-flag" });
         sync.closeRemote();
-        console.log(`Pulled: ${result.pulled} | Skipped: ${result.skipped} | Conflicts: ${result.conflicts.length}`);
+        const projParts = (result.projectsPulled || 0) > 0 ? ` | Projects pulled: ${result.projectsPulled}` : "";
+        console.log(`Pulled: ${result.pulled} | Skipped: ${result.skipped} | Conflicts: ${result.conflicts.length}${projParts}`);
         if (result.errors.length > 0) {
             console.log("\nErrors:");
             for (const e of result.errors)
@@ -2670,7 +2720,7 @@ remoteCmd
     .action(async (opts) => {
     let centralDb = null;
     try {
-        centralDb = GnosysDB.openCentral();
+        centralDb = GnosysDB.openLocal();
         if (!centralDb.isAvailable()) {
             if (!opts.auto)
                 console.error("Central DB not available.");
@@ -2690,7 +2740,10 @@ remoteCmd
         });
         sync.closeRemote();
         if (!opts.auto || result.conflicts.length > 0 || result.errors.length > 0) {
-            console.log(`Pushed: ${result.pushed} | Pulled: ${result.pulled} | Conflicts: ${result.conflicts.length}`);
+            const pp = result.projectsPushed || 0;
+            const pl = result.projectsPulled || 0;
+            const projParts = (pp + pl) > 0 ? ` | Projects: ↑${pp}/↓${pl}` : "";
+            console.log(`Pushed: ${result.pushed} | Pulled: ${result.pulled} | Conflicts: ${result.conflicts.length}${projParts}`);
             if (result.errors.length > 0) {
                 console.log("\nErrors:");
                 for (const e of result.errors)
@@ -2717,7 +2770,7 @@ remoteCmd
     .action(async (memoryId, opts) => {
     let centralDb = null;
     try {
-        centralDb = GnosysDB.openCentral();
+        centralDb = GnosysDB.openLocal();
         if (!centralDb.isAvailable()) {
             console.error("Central DB not available.");
             process.exit(1);
@@ -2759,7 +2812,7 @@ remoteCmd
     .action(async (opts) => {
     let centralDb = null;
     try {
-        centralDb = GnosysDB.openCentral();
+        centralDb = GnosysDB.openLocal();
         if (!centralDb.isAvailable()) {
             console.error("Central DB not available.");
             process.exit(1);