studiograph 1.3.48-next.16 → 1.3.48-next.160

package/README.md

@@ -31,22 +31,27 @@ To create repos on GitHub during init:
 studiograph init "My Studio" --github --github-org my-org
 ```
 
-### Join an Existing Workspace
+### Clone an Existing Workspace
 
 ```bash
-studiograph join https://github.com/my-org/.studiograph.git
+studiograph clone https://studiograph.example.com /path/to/local/copy
 ```
 
-This clones the config repo, identifies your role from the team roster, and clones all repos you have access to.
+Authenticates as the workspace owner against a running Studiograph server,
+mints a per-machine API token, persists it to `~/.studiograph/user.json`, and
+clones every accessible repo. Subsequent `pull`/`push` runs are non-interactive
+via the stored token.
 
-### Start the Agent
+### Boot the Workspace
 
 ```bash
 cd my-studio
-studiograph start
+studiograph serve
 ```
 
-On first run, you'll be prompted to select an AI provider and model. The agent provides a chat interface where you can create, search, and manage entities across your knowledge graph.
+This starts the local HTTP server + opens the web UI. The web chat panel is the canonical agent surface: a richer chat UX, real-time graph view, and inline editor. On first boot you'll be prompted to set up an AI provider and model.
+
+If you want a terminal-side agent (Claude Desktop / Cursor integration), run `studiograph mcp` — it exposes the same toolset over MCP.
 
 ## How It Works
 
@@ -57,15 +62,15 @@ A Studiograph workspace is a directory containing a `.studiograph/` configuratio
 ```
 my-studio/
 ├── .studiograph/           # Config repo (workspace.json, team roster, migrations)
-├── acme-rebrand/           # Collection (client project)
-├── website-redesign/       # Collection (another project)
-├── team-knowledge/         # Collection (processes, standards)
+├── acme-rebrand/           # Folder (client project)
+├── website-redesign/       # Folder (another project)
+├── team-knowledge/         # Folder (processes, standards)
 └── private/                # Local-only, gitignored
 ```
 
-### Collections
+### Folders
 
-Each subdirectory is a **collection** — a Git repo containing related entities. Collections are lightweight and flexible: one per project, one for team knowledge, one for business operations, or however your team thinks.
+Each subdirectory is a **folder** — a Git repo containing related entities. Folders are lightweight and flexible: one per project, one for team knowledge, one for business operations, or however your team thinks.
 
 ### Entities
 
@@ -118,14 +123,13 @@ There are 17 built-in entity types (project, meeting, person, organization, deci
 | Command | Description |
 |---------|-------------|
 | `studiograph init <team-name> [dir]` | Initialize a new workspace |
-| `studiograph join <url> [dir]` | Join an existing workspace via GitHub URL |
-| `studiograph auth` | Manage GitHub authentication |
+| `studiograph clone <url> [dir]` | Clone an existing workspace from a running server |
 
 ### Daily Workflow
 
 | Command | Description |
 |---------|-------------|
-| `studiograph start` | Launch the AI agent chat interface |
+| `studiograph serve` | Boot the local HTTP server + open the web UI |
 | `studiograph pull` | Pull latest changes from remote |
 | `studiograph push` | Push local commits to remote |
 
@@ -133,7 +137,7 @@ There are 17 built-in entity types (project, meeting, person, organization, deci
 
 | Command | Description |
 |---------|-------------|
-| `studiograph collection` | Manage collections (add, list, rename, remove) |
+| `studiograph folder` | Manage folders (add, list, rename, remove) |
 | `studiograph provision` | Push workspace config to GitHub as a separate repo |
 | `studiograph members` | Manage team members and roles |
 | `studiograph index` | Rebuild search index |
@@ -190,7 +194,7 @@ Studiograph exposes a [Model Context Protocol](https://modelcontextprotocol.io/)
 
 If you're running from the workspace directory, you can omit the path: `studiograph mcp`.
 
-MCP tools available: `list_repos`, `list_entities`, `get_entity`, `search_entities`, `create_entity`, `update_entity`, `delete_entity`.
+MCP tools available: `list_repos`, `create_repo`, `list_entities`, `get_entity`, `search_entities`, `create_entity`, `update_entity`, `delete_entity`.
 
 ### Third-Party Connectors
 

package/dist/agent/agent-pool.d.ts

@@ -1,7 +1,7 @@
 /**
  * Agent Pool — manages per-session Agent instances for concurrent access.
  *
- * Each session (collection chat, private chat, capture) gets its own Agent
+ * Each session (folder chat, private chat, capture) gets its own Agent
  * with independent conversation history. Shared resources (tools, system
  * prompt, model) are created once and passed to each new agent.
  *
@@ -15,12 +15,37 @@ export interface AgentContext {
     user: AuthUser | null;
     onHighlight?: ((ids: string[]) => void) | null;
     onMutation?: ((m: MutationEvent) => void) | null;
+    /**
+     * Called by tool wrappers at the start (`enter`) and end (`leave`) of any
+     * mutation that targets a folder. Powers the "X's agent is acting" sidebar
+     * chip via wsHub.handleAgentActivity. Optional — no-op if unset.
+     */
+    onAgentActivity?: ((action: 'enter' | 'leave' | 'heartbeat', repo: string) => void) | null;
+    /**
+     * Wired only by the quick-capture flow. When the agent calls the
+     * `nothing_to_capture` tool, this receives the structured reason so the
+     * UI can render a toast without going through freeform assistant prose
+     * (which is variable-quality and leaks the followups marker).
+     */
+    onNothingToCapture?: ((reason: string) => void) | null;
 }
 export interface SharedAgentConfig {
     /** Factory to create a fresh Agent instance with tools, prompt, and model. */
     createAgent: (userId?: number) => Agent;
-    /** Callback to load custom tools async (called once per new agent). */
-    loadCustomTools?: (agent: Agent) => void;
+    /**
+     * Callback to load custom tools async (called once per new agent). The
+     * pool passes the session's `userId` so per-user MCP connector OAuth
+     * tokens can be resolved at tool-build time — without this, the agent
+     * runtime can't read tokens stored under `(user, connector)`.
+     *
+     * Must return a Promise that resolves when tool loading is done (or
+     * rejects on failure — the pool catches and treats it as "load gave
+     * up, proceed with bundled tools"). `withAgent` awaits this on the
+     * first chat call for the session so the first turn doesn't race
+     * against still-loading MCP connector tools. The promise resolves
+     * once and subsequent turns see it as a no-op.
+     */
+    loadCustomTools?: (agent: Agent, userId?: number) => Promise<void>;
     /** Base sessions directory. */
     sessionsDir: string;
 }
@@ -52,6 +77,30 @@ export declare class AgentPool {
     getAgent(sessionId: string): Agent | null;
     /** Abort the agent for a session. */
     abort(sessionId: string): void;
+    /**
+     * Evict every cached agent instance. Persists each session's history
+     * first so no in-memory transcript is lost. Next chat for any session
+     * spins up a fresh agent (via `createAgent` from the config), which
+     * re-reads model/provider/api_key via `resolveApiKey` — picking up
+     * whatever the store now has.
+     *
+     * Used as the eviction hook on secret/setting mutations: when the
+     * operator rotates an API key or switches providers via Settings UI,
+     * the running agent's captured apiKey is stale until restart. This
+     * is the surgical fix instead of restarting the whole process.
+     */
+    invalidateAll(): void;
+    /**
+     * Evict every pool entry owned by a specific user. Used as the eviction
+     * hook on per-user OAuth mutations: when a user OAuths a new connector
+     * (or revokes one), their running agent's tool list — captured at
+     * createAgentInstance time — no longer matches reality. Sessions
+     * belonging to OTHER users stay in the pool untouched.
+     *
+     * Saved sessions are written to disk before removal, same as
+     * `invalidateAll`, so no transcript is lost.
+     */
+    invalidateUser(userId: number): void;
     /** Save all sessions and stop the reaper. */
     shutdown(): Promise<void>;
     /** Clear all saved session files for a user. */

package/dist/agent/agent-pool.js

@@ -1,7 +1,7 @@
 /**
  * Agent Pool — manages per-session Agent instances for concurrent access.
  *
- * Each session (collection chat, private chat, capture) gets its own Agent
+ * Each session (folder chat, private chat, capture) gets its own Agent
  * with independent conversation history. Shared resources (tools, system
  * prompt, model) are created once and passed to each new agent.
  *
@@ -37,8 +37,14 @@ export class AgentPool {
      */
     async withAgent(sessionId, ctx, fn, opts) {
         const entry = this.getOrCreate(sessionId, opts?.userId, opts?.fallbackHistory);
-        // Chain on the session's lock to serialize calls
+        // Chain on the session's lock to serialize calls. Also await
+        // toolsLoaded so the first turn's prompt-to-Anthropic sees the
+        // full tool list (bundled + custom + per-user connector). On
+        // subsequent turns this promise is already resolved — no wait.
+        // Toolloading errors were caught upstream; the await is purely
+        // for ordering, never throws.
         const result = entry.lock.then(async () => {
+            await entry.toolsLoaded;
             entry.lastUsedAt = Date.now();
             this.contextMap.set(sessionId, ctx);
             try {
@@ -62,6 +68,43 @@ export class AgentPool {
     abort(sessionId) {
         this.pool.get(sessionId)?.agent.abort();
     }
+    /**
+     * Evict every cached agent instance. Persists each session's history
+     * first so no in-memory transcript is lost. Next chat for any session
+     * spins up a fresh agent (via `createAgent` from the config), which
+     * re-reads model/provider/api_key via `resolveApiKey` — picking up
+     * whatever the store now has.
+     *
+     * Used as the eviction hook on secret/setting mutations: when the
+     * operator rotates an API key or switches providers via Settings UI,
+     * the running agent's captured apiKey is stale until restart. This
+     * is the surgical fix instead of restarting the whole process.
+     */
+    invalidateAll() {
+        for (const entry of this.pool.values()) {
+            this.saveSession(entry);
+        }
+        this.pool.clear();
+    }
+    /**
+     * Evict every pool entry owned by a specific user. Used as the eviction
+     * hook on per-user OAuth mutations: when a user OAuths a new connector
+     * (or revokes one), their running agent's tool list — captured at
+     * createAgentInstance time — no longer matches reality. Sessions
+     * belonging to OTHER users stay in the pool untouched.
+     *
+     * Saved sessions are written to disk before removal, same as
+     * `invalidateAll`, so no transcript is lost.
+     */
+    invalidateUser(userId) {
+        for (const [sessionId, entry] of this.pool.entries()) {
+            if (entry.userId === userId) {
+                this.saveSession(entry);
+                this.pool.delete(sessionId);
+                this.contextMap.delete(sessionId);
+            }
+        }
+    }
     /** Save all sessions and stop the reaper. */
     async shutdown() {
         if (this.reapTimer) {
@@ -105,20 +148,57 @@ export class AgentPool {
             return existing;
         // Create a fresh agent instance (pass userId for per-user context like briefing)
         const agent = this.config.createAgent(userId);
-        this.config.loadCustomTools?.(agent);
+        // Kick off async tool loading. The returned promise gets stashed on
+        // the pool entry so the first withAgent call can await it — that's
+        // what closes the timing race between agent construction and the
+        // user's first chat turn referencing a connector tool. If the
+        // callback returns undefined (legacy or test surfaces that don't
+        // need to gate on it), treat it as already-resolved.
+        const toolsLoaded = (this.config.loadCustomTools?.(agent, userId) ?? Promise.resolve()).catch((err) => {
+            // Swallow the rejection here — the agent should proceed with
+            // whatever subset of tools landed. The orchestrator's own
+            // catch path already logged the underlying failure.
+            // eslint-disable-next-line no-console
+            console.warn(`[agent-pool] tool loading rejected, proceeding with bundled tools: ${err instanceof Error ? err.message : err}`);
+        });
         // Try loading session from disk
         const loaded = this.loadSession(agent, sessionId, userId);
-        // Fallback: inject history as context if no saved session
+        // Fallback: rebuild the transcript as proper role-tagged messages when
+        // the saved session file is missing (cleared, corrupted, or first turn
+        // on a fresh container). The previous implementation flattened the
+        // entire history into a single role: 'user' message with "Assistant:" /
+        // "User:" prefixes embedded as plain text — the model then had to parse
+        // those textual prefixes to know what was its own output, and would
+        // sometimes mis-attribute its prior turns to the user (e.g. "you
+        // mentioned that Watowa consults" when the user had just said "we
+        // consult on..."). Mapping each turn to its actual role tag lets the
+        // model distinguish reliably without parsing-by-prefix.
         if (!loaded && fallbackHistory && fallbackHistory.length > 0) {
-            const transcript = fallbackHistory
-                .map(m => `${m.role === 'assistant' ? 'Assistant' : 'User'}: ${m.content}`)
-                .join('\n\n');
-            const contextMsg = {
-                role: 'user',
-                content: [{ type: 'text', text: `[Prior conversation context]\n\n${transcript}` }],
-                timestamp: Date.now(),
-            };
-            agent.replaceMessages([contextMsg]);
+            const model = agent.state.model;
+            const baseTime = Date.now() - fallbackHistory.length * 1000;
+            agent.state.messages = fallbackHistory.map((m, i) => {
+                const timestamp = baseTime + i * 1000;
+                if (m.role === 'assistant') {
+                    return {
+                        role: 'assistant',
+                        content: [{ type: 'text', text: m.content }],
+                        api: model.api,
+                        provider: model.provider,
+                        model: model.id,
+                        usage: {
+                            input: 0, output: 0, cacheRead: 0, cacheWrite: 0, totalTokens: 0,
+                            cost: { input: 0, output: 0, cacheRead: 0, cacheWrite: 0, total: 0 },
+                        },
+                        stopReason: 'stop',
+                        timestamp,
+                    };
+                }
+                return {
+                    role: 'user',
+                    content: [{ type: 'text', text: m.content }],
+                    timestamp,
+                };
+            });
         }
         const entry = {
             agent,
@@ -126,6 +206,7 @@ export class AgentPool {
             userId,
             lastUsedAt: Date.now(),
             lock: Promise.resolve(),
+            toolsLoaded,
         };
         this.pool.set(sessionId, entry);
         return entry;
@@ -140,7 +221,7 @@ export class AgentPool {
             try {
                 const data = JSON.parse(readFileSync(sessionPath, 'utf-8'));
                 if (Array.isArray(data.messages) && data.messages.length > 0) {
-                    agent.replaceMessages(data.messages);
+                    agent.state.messages = data.messages;
                     return true;
                 }
             }

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package/dist/agent/followups.d.ts

@@ -0,0 +1,34 @@
+/**
+ * Follow-up suggestion marker parsing.
+ *
+ * The system prompt instructs the agent to end every response with an HTML
+ * comment of the form:
+ *
+ *   <!-- followups: ["prompt 1", "prompt 2", "prompt 3"] -->
+ *
+ * Each transport (web, CLI, MCP) must strip this marker from the content it
+ * displays and surface the suggestions in whatever form fits its UI — chips
+ * in the web client, a dim numbered list in the CLI, a `suggestions` field
+ * in MCP, etc.
+ *
+ * Keep the parser in one place so a new transport can't silently leak the
+ * raw marker.
+ */
+export interface ParsedFollowups {
+    /** Response content with the marker removed and trailing whitespace trimmed. */
+    content: string;
+    /** Parsed suggestions, if the marker was present and valid JSON. */
+    suggestions?: string[];
+}
+/**
+ * Parse a raw agent response and split it into clean content plus optional
+ * follow-up suggestions. Malformed markers are left in place (the caller can
+ * choose to strip or render as-is), matching the existing web behaviour.
+ */
+export declare function parseFollowups(raw: string): ParsedFollowups;
+/**
+ * Return true if `text` contains an *unclosed* followups marker — used by
+ * streaming consumers to know whether to defer rendering the tail of a
+ * delta until the closing `-->` arrives.
+ */
+export declare function hasOpenFollowupsMarker(text: string): boolean;

package/dist/agent/followups.js

@@ -0,0 +1,52 @@
+/**
+ * Follow-up suggestion marker parsing.
+ *
+ * The system prompt instructs the agent to end every response with an HTML
+ * comment of the form:
+ *
+ *   <!-- followups: ["prompt 1", "prompt 2", "prompt 3"] -->
+ *
+ * Each transport (web, CLI, MCP) must strip this marker from the content it
+ * displays and surface the suggestions in whatever form fits its UI — chips
+ * in the web client, a dim numbered list in the CLI, a `suggestions` field
+ * in MCP, etc.
+ *
+ * Keep the parser in one place so a new transport can't silently leak the
+ * raw marker.
+ */
+/** Matches the trailing followups HTML comment at end of text (with optional trailing whitespace). */
+const FOLLOWUPS_RE = /<!--\s*followups:\s*(\[[\s\S]*?\])\s*-->\s*$/;
+/**
+ * Parse a raw agent response and split it into clean content plus optional
+ * follow-up suggestions. Malformed markers are left in place (the caller can
+ * choose to strip or render as-is), matching the existing web behaviour.
+ */
+export function parseFollowups(raw) {
+    const match = raw.match(FOLLOWUPS_RE);
+    if (!match)
+        return { content: raw };
+    try {
+        const parsed = JSON.parse(match[1]);
+        if (!Array.isArray(parsed) || !parsed.every((s) => typeof s === 'string')) {
+            return { content: raw };
+        }
+        const content = raw.slice(0, match.index).trimEnd();
+        return { content, suggestions: parsed };
+    }
+    catch {
+        return { content: raw };
+    }
+}
+/**
+ * Return true if `text` contains an *unclosed* followups marker — used by
+ * streaming consumers to know whether to defer rendering the tail of a
+ * delta until the closing `-->` arrives.
+ */
+export function hasOpenFollowupsMarker(text) {
+    const lastOpen = text.lastIndexOf('<!--');
+    if (lastOpen < 0)
+        return false;
+    const lastClose = text.lastIndexOf('-->');
+    return lastClose < lastOpen;
+}
+//# sourceMappingURL=followups.js.map

package/dist/agent/followups.js.map

@@ -0,0 +1 @@
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package/dist/agent/orchestrator.d.ts

@@ -9,6 +9,7 @@ import { WorkspaceManager } from '../core/workspace-manager.js';
 import { WorkspaceConfig } from '../core/types.js';
 import { GitUser } from '../services/git.js';
 import { type MutationEvent } from './tools/graph-tools.js';
+import { AuthService } from '../services/auth-service.js';
 import type { AuthUser } from '../services/auth-service.js';
 import { AgentPool } from './agent-pool.js';
 export interface AgentConfig {
@@ -23,8 +24,24 @@ export interface AgentConfig {
     recentMemory?: string;
     /** Shared WorkspaceManager instance (used by server to share state with agent). */
     workspaceManager?: WorkspaceManager;
-    /** Shared MessageService instance (for searching collection messages). */
-    messageService?: import('../services/message-service.js').MessageService;
+    /**
+     * Shared AuthService — pass the route-level instance so the
+     * orchestrator participates in the same OAuth-mutation pubsub and uses
+     * the master-key-wired crypto path for `oauth_tokens` reads.
+     *
+     * Without this, the orchestrator constructs a fresh AuthService that
+     * (a) has no master key, so reads of encrypted oauth_tokens rows
+     * throw; (b) subscribes to a different pubsub channel than the one
+     * `connectors-api.ts` fires, so OAuth-mutation invalidations never
+     * reach the agent pool. Phase 8 (May 11 2026) wired crypto into the
+     * route-level AuthService but missed this instance — latent until
+     * the 2026-05-13 per-user OAuth runtime wiring made the orchestrator
+     * actually read encrypted oauth_tokens.
+     *
+     * Tests and CLI surfaces still construct their own — back-compat
+     * fallback below.
+     */
+    authService?: AuthService;
 }
 export interface AgentResponse {
     content: string;
@@ -44,7 +61,6 @@ export declare class AgentOrchestrator {
     private toolsDirs;
     private registryRef;
     private authService;
-    private messageService;
     private recentMemory?;
     private sessionsDir;
     private _currentUser;
@@ -63,12 +79,32 @@ export declare class AgentOrchestrator {
      * Runs async after construction — custom tools may not be available for the
      * very first message if initialisation is extremely fast, but in practice
      * the first user message arrives well after startup.
+     *
+     * `userId` is forwarded into `ConnectorManager.buildTools` so per-user MCP
+     * OAuth tokens are resolved at tool-build time. Without it the runtime
+     * silently falls back to workspace-shared static headers (the deferred
+     * gap before 2026-05-13). The agent pool keys agents per-session and
+     * supplies the session's userId on creation; CLI / non-interactive
+     * spawns pass `undefined` and intentionally land on the workspace
+     * fallback.
      */
     private loadCustomToolsAsync;
     /**
      * Build the full system prompt: base prompt + eager skill content + skill index.
      */
     private buildSystemPrompt;
+    /**
+     * Enumerate skill entities across all folders the user can access. Each
+     * skill becomes a SkillMeta with a `graph://<repo>/<id>` sentinel
+     * entrypoint. Priority order: user's private folder first, then shared
+     * folders alphabetically. First occurrence of a given name wins.
+     */
+    private getPromptRepoScope;
+    private enumerateGraphSkills;
+    /**
+     * Load the markdown body of a skill entity by (repo, id).
+     */
+    private readGraphSkillBody;
     /**
      * Build a workspace identity section from graph entities.
      * Reads organization, person, practice-area, and guideline entries
@@ -76,6 +112,13 @@ export declare class AgentOrchestrator {
      * Returns null if no organization entries exist.
      */
     private buildWorkspaceIdentity;
+    /**
+     * Per-repo subfolder summary for the system prompt. Lists each accessible
+     * repo with up to MAX_PER_REPO subfolder paths so the agent can route new
+     * entries into existing folders without calling list_folders for every
+     * decision. Refresh cadence is per-session (system prompt is built once).
+     */
+    private buildFolderInventory;
     /**
      * Fallback system prompt when prompts/system.md is not found.
      */
@@ -118,7 +161,7 @@ export declare class AgentOrchestrator {
      */
     getRepoNames(): string[];
     /**
-     * Set the current authenticated user for per-collection access filtering.
+     * Set the current authenticated user for per-folder access filtering.
      * Called per-request by the chat endpoint. Null = full access (API key / open mode).
      */
     setCurrentUser(user: AuthUser | null): void;