studiograph 1.3.3 → 1.3.5

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 type { AuthUser } from '../services/auth-service.js';
 export interface AgentConfig {
     workspacePath: string;
     workspaceConfig: WorkspaceConfig;
@@ -19,6 +20,8 @@ export interface AgentConfig {
     toolsDirs?: string[];
     /** Recent daily memory content (today + yesterday) injected into system prompt. */
     recentMemory?: string;
+    /** Shared WorkspaceManager instance (used by server to share state with agent). */
+    workspaceManager?: WorkspaceManager;
 }
 export interface AgentResponse {
     content: string;
@@ -39,6 +42,8 @@ export declare class AgentOrchestrator {
     private registryRef;
     private _highlightCallback;
     private _mutationCallback;
+    private _currentUser;
+    private authService;
     private recentMemory?;
     private currentSessionId;
     private sessionsDir;
@@ -84,6 +89,11 @@ export declare class AgentOrchestrator {
      * Get repository names
      */
     getRepoNames(): string[];
+    /**
+     * Set the current authenticated user for per-collection access filtering.
+     * Called per-request by the chat endpoint. Null = full access (API key / open mode).
+     */
+    setCurrentUser(user: AuthUser | null): void;
     /**
      * Set a callback for highlight_entities tool events (used by SSE streaming).
      */

package/dist/agent/orchestrator.js

@@ -14,6 +14,7 @@ import { getModel } from '@mariozechner/pi-ai';
 import { Agent } from '@mariozechner/pi-agent-core';
 import { WorkspaceManager } from '../core/workspace-manager.js';
 import { createGraphTools } from './tools/graph-tools.js';
+import { createSyncTools } from './tools/sync-tools.js';
 import { loadSkillIndex, buildSkillIndexPrompt, loadEagerSkills } from './skill-loader.js';
 import { createLoadSkillTool } from './tools/load-skill.js';
 import { loadCustomTools } from './tools/tool-loader.js';
@@ -22,6 +23,7 @@ import { buildConnectorRegistry, createConnectorTools } from './tools/connector-
 import { createFsTools } from './tools/fs-tools.js';
 import { createOpsTools } from './tools/ops-tools.js';
 import { createPermissionTools } from './tools/permission-tools.js';
+import { AuthService } from '../services/auth-service.js';
 import { loadUserConfig, resolveApiKey, resolveProvider, resolveModelId } from '../core/user-config.js';
 export class AgentOrchestrator {
     workspacePath;
@@ -34,6 +36,8 @@ export class AgentOrchestrator {
     registryRef = { registry: null };
     _highlightCallback = null;
     _mutationCallback = null;
+    _currentUser = null;
+    authService;
     recentMemory;
     currentSessionId = null;
     sessionsDir;
@@ -42,6 +46,7 @@ export class AgentOrchestrator {
         this.config = config.workspaceConfig;
         this.gitUser = config.gitUser;
         this.recentMemory = config.recentMemory;
+        this.authService = new AuthService(config.workspacePath);
         this.sessionsDir = join(homedir(), '.studiograph', 'sessions');
         // Priority (highest → lowest): user > workspace > bundled > app
         // First-seen name wins in the loader, so earlier dirs override later ones.
@@ -52,8 +57,8 @@ export class AgentOrchestrator {
         const bundledSkillsDir = join(__dirname, 'skills');
         this.skillsDirs = [userSkillsDir, workspaceSkillsDir, bundledSkillsDir, ...(config.skillsDirs ?? [])];
         this.toolsDirs = [userToolsDir, workspaceToolsDir, ...(config.toolsDirs ?? [])];
-        // Initialize workspace manager
-        this.workspaceManager = new WorkspaceManager(this.workspacePath, this.config, this.gitUser);
+        // Use shared workspace manager if provided, otherwise create one
+        this.workspaceManager = config.workspaceManager ?? new WorkspaceManager(this.workspacePath, this.config, this.gitUser);
         // Initialize Pi-Mono agent (async tools loaded in createAgent)
         this.agent = this.createAgent();
     }
@@ -74,11 +79,10 @@ export class AgentOrchestrator {
         const skillIndex = loadSkillIndex(this.skillsDirs);
         // Build tools first so we can auto-generate the tool reference for the prompt
         const tools = [
-            ...createGraphTools(this.workspaceManager, this.gitUser, this.workspacePath, this.emitHighlight.bind(this), this.emitMutation.bind(this)),
-            // Sync tools gated for MVP — re-enable when sync pipeline is production-ready
-            // ...createSyncTools(this.workspacePath, this.config, this.registryRef),
+            ...createGraphTools(this.workspaceManager, this.gitUser, this.workspacePath, this.emitHighlight.bind(this), this.emitMutation.bind(this), () => this._currentUser, this.authService),
+            ...createSyncTools(this.workspacePath, this.config, this.registryRef),
             ...createOpsTools(this.workspacePath, this.config),
-            ...createPermissionTools(this.config),
+            ...createPermissionTools(this.authService),
             ...createFsTools(),
             createLoadSkillTool(skillIndex),
         ];
@@ -106,7 +110,7 @@ export class AgentOrchestrator {
         const context = { workspaceManager: this.workspaceManager, gitUser: this.gitUser };
         Promise.all([
             loadCustomTools(this.toolsDirs, context),
-            ConnectorManager.buildTools(ConnectorManager.loadConfigs()),
+            ConnectorManager.buildTools(ConnectorManager.loadConfigs(this.workspacePath)),
         ]).then(([customTools, connectorTools]) => {
             const extra = [...customTools];
             if (connectorTools.length > 0) {
@@ -162,6 +166,14 @@ export class AgentOrchestrator {
             .join('\n\n');
         base = base.replace('{{TOOL_REFERENCE}}', toolRef);
         const parts = [base.trim()];
+        // Inject workspace ABOUT.md as organizational context
+        const aboutPath = join(this.workspacePath, '.studiograph', 'ABOUT.md');
+        if (existsSync(aboutPath)) {
+            const aboutContent = readFileSync(aboutPath, 'utf-8');
+            if (aboutContent.trim()) {
+                parts.push(`## Workspace Identity\n\n${aboutContent}`);
+            }
+        }
         // Append workspace schema extensions (org-specific fields and custom types)
         const schemaSection = this.workspaceManager.getSchemaRegistry().toPromptSection();
         if (schemaSection) {
@@ -267,6 +279,13 @@ ${repoList}`;
     getRepoNames() {
         return this.workspaceManager.getRepoNames();
     }
+    /**
+     * Set the current authenticated user for per-collection access filtering.
+     * Called per-request by the chat endpoint. Null = full access (API key / open mode).
+     */
+    setCurrentUser(user) {
+        this._currentUser = user;
+    }
     /**
      * Set a callback for highlight_entities tool events (used by SSE streaming).
      */

package/dist/agent/orchestrator.js.map

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package/dist/agent/skills/sync-configuration.md

@@ -42,14 +42,13 @@ Use this reference when helping users build or modify source configs at `.studio
 | `list_params` | No | Extra params for list tool. Pass array for multiple list calls merged |
 | `directory_patterns` | No | Directory patterns for file sources (frontmatter/unstructured) |
 | `write_mode` | No | `"entity"` (default, `id/main.md` folder) or `"collection"` (flat `id.md` file) |
-| `co_locate` | No | Co-locate as sub-content inside parent entity folder |
 | `list_tool` | No | Explicit MCP tool name for listing records (bypasses heuristic matching) |
 | `read_tool` | No | Explicit MCP tool name for reading records (bypasses heuristic matching) |
 
 ## Extraction Modes
 
 - **`structured`** — API JSON → field_map → frontmatter. No LLM. For Pipedrive, Linear, Granola, Asana.
-- **`frontmatter`** — Markdown files with YAML → field_map. No LLM. For Obsidian. Supports `_filename` and `_body` sentinels.
+- **`frontmatter`** — Markdown files with YAML → field_map. No LLM. Supports `_filename` and `_body` sentinels.
 - **`unstructured`** — Freeform text → LLM extraction. Slow, expensive. Last resort when no structured metadata exists.
 
 ## Field Map Syntax
@@ -80,33 +79,12 @@ Result: `["[[alice]]", ...]`
 | `wikilink` | `"Acme Corp"` | `"[[acme-corp]]"` |
 | `wikilink-array` | `["Alice", "Bob"]` | `["[[alice]]", "[[bob]]"]` |
 
-## Co-Location
-
-Writes entities as sub-content files inside a parent entity folder instead of standalone entity folders.
-
-**Config:** Add `co_locate` to a mapping:
-```json
-{
-  "co_locate": { "parent_field": "project", "subfolder": "tasks" },
-  "field_map": { "project": { "field": "project", "transform": "wikilink" } }
-}
-```
-
-**Result path:** `{target_repo}/{parent_id}/{subfolder}/{entity_id}.md`
-Example: `projects/cooper-hewitt-brand-refresh/tasks/sch-101.md`
-
-**Rules:**
-- `parent_field` must be a wikilink target in `field_map` so the reference is available
-- Entities without a parent value are **skipped** (not an error)
-- Co-located files are sub-content, not graph entities (no `entity_id/main.md` folder)
-- `target_repo` should be the repo where the **parent** entities live
-
 ## Write Mode
 
 Controls how entities are written to disk:
 
-- **`entity`** (default) — `repo/entity-id/main.md` folder. Fully indexed, supports sub-content. Use for core types (projects, clients, people).
-- **`collection`** — `repo/entity-id.md` flat file. Simpler, no folder overhead. Use for high-volume types (meetings, notes, references).
+- **`entity`** (default) — `repo/entity-type/entity-id.md` in a typed subfolder. Fully indexed. Use for core types (projects, clients, people).
+- **`collection`** — `repo/entity-id.md` flat file at collection root. Use for high-volume types (meetings, notes, references).
 
 ## Explicit MCP Tool Selection
 
@@ -127,14 +105,11 @@ When omitted, the pipeline uses heuristic matching (looking for tools containing
 |--------|----------|-------|
 | **Pipedrive** | deal→project, person→person, org→client | Ready to sync |
 | **Granola** | document→meeting | `fetch_details: true`, `list_limit: 1000` |
-| **Linear** | issue→task (co-located under projects), project→project | Issues use `co_locate` |
+| **Linear** | issue→task, project→project | Tasks written to typed subfolder |
 | **Asana** | task→task, project→project | Needs `list_params: { workspace: "GID" }` |
-| **Obsidian** | Example mappings only (`.template` file) | Needs customization per vault |
 
 ## Configuration Patterns
 
-**Adding co-location to any mapping:** Add `co_locate: { parent_field, subfolder }` and ensure `parent_field` is a wikilink target in `field_map`.
-
 **Multiple list calls:** Set `list_params` as an array: `[{ workspace: "123", archived: false }, { workspace: "123", archived: true }]`
 
 **Custom source (no built-in):** Create a source config with `entity_mappings` from scratch. Choose extraction_mode, define field_map targeting entity schema fields, set target_repo.

package/dist/agent/skills/sync-setup.md

@@ -6,7 +6,7 @@ loading: eager
 
 # Entity Sync
 
-You can sync data from external sources (Linear, Pipedrive, Granola, Obsidian, etc.) into the knowledge graph using the sync tools.
+You can sync data from external sources (Linear, Pipedrive, Granola, Google Drive, Asana, etc.) into the knowledge graph using the sync tools.
 
 ## First-Time Setup
 
@@ -46,7 +46,7 @@ When a user asks to adjust, change, or view a source config, **immediately call
 3. Build the updated `entity_mappings` array (you must pass the complete array — it replaces, not merges)
 4. `sync_setup_source({ name: "...", entity_mappings: [...], force: true })` — overwrite with updated config
 
-Common adjustments: changing `field_map` entries, adding/removing entity mappings, changing `target_repo`, adding `co_locate`, switching `write_mode`, adjusting `status_map`, adding `list_tool`/`read_tool`.
+Common adjustments: changing `field_map` entries, adding/removing entity mappings, changing `target_repo`, switching `write_mode`, adjusting `status_map`, adding `list_tool`/`read_tool`.
 
 ## Repeat Sync Flow
 
@@ -71,8 +71,6 @@ After `sync_apply`, explain what happened to the user:
 
 - **"Uncommitted changes"** — sync requires a clean working tree. Tell the user to commit or stash changes first, or use `--force` to override
 - **"Connector not found"** — the connector isn't set up. User must run `studiograph connector add <name>` in terminal
-- **Entities skipped during apply** — for co-located entities, check that the `parent_field` has a value in the extracted frontmatter. Missing parent = skip.
-- **Obsidian template file** — Obsidian creates a `.template` file instead of default mappings (every vault is different). Tell the user to copy mappings from the template into the source config and adjust `directory_patterns` and `field_map` for their vault.
 
 ## Important Rules
 

package/dist/agent/tools/graph-tools.d.ts

@@ -8,6 +8,8 @@
  * - Upload assets
  */
 import { WorkspaceManager } from '../../core/workspace-manager.js';
+import type { AuthUser } from '../../services/auth-service.js';
+import type { AuthService } from '../../services/auth-service.js';
 /**
  * Helper to wrap tool results in AgentToolResult format
  */
@@ -31,7 +33,7 @@ export declare function createGraphTools(workspaceManager: WorkspaceManager, git
     id: string;
     name: string;
     email: string;
-}, workspacePath?: string, onHighlight?: (ids: string[]) => void, onMutation?: (m: MutationEvent) => void): ({
+}, workspacePath?: string, onHighlight?: (ids: string[]) => void, onMutation?: (m: MutationEvent) => void, getCurrentUser?: () => AuthUser | null, authService?: AuthService | null): ({
     name: string;
     label: string;
     description: string;
@@ -50,10 +52,12 @@ export declare function createGraphTools(workspaceManager: WorkspaceManager, git
     parameters: import("@sinclair/typebox").TObject<{
         name: import("@sinclair/typebox").TString;
         description: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+        private: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
     }>;
     execute: (toolCallId: string, params: {
         name: string;
         description?: string;
+        private?: boolean;
     }) => Promise<{
         content: {
             type: "text";

package/dist/agent/tools/graph-tools.js

@@ -30,7 +30,58 @@ function cleanData(data) {
     const { entity_type, entity_id, ...rest } = data;
     return rest;
 }
-export function createGraphTools(workspaceManager, gitUser, workspacePath, onHighlight, onMutation) {
+/**
+ * Per-request user context for collection access filtering.
+ * When getCurrentUser returns a non-admin user, tools filter results
+ * to only collections the user has been granted access to.
+ */
+/** Check if a user can see a private repo (only the owner can). */
+function canSeePrivateRepo(repoConfig, user) {
+    if (!repoConfig?.private)
+        return true;
+    if (!user)
+        return !repoConfig.owner_id; // API key / open mode — only if no owner set
+    if (!repoConfig.owner_id)
+        return false; // Private without owner — hidden from all users
+    return user.id === repoConfig.owner_id;
+}
+function getAccessibleRepoNames(workspaceManager, getCurrentUser, authService) {
+    const user = getCurrentUser();
+    if (!user)
+        return null; // API key / open mode → no filtering
+    if (!authService)
+        return null;
+    const allRepos = workspaceManager.getAllRepoConfigs();
+    if (user.role === 'admin') {
+        // Admins see all non-private + their own private repos
+        const hidden = allRepos.filter(r => !canSeePrivateRepo(r, user)).map(r => r.name);
+        if (hidden.length === 0)
+            return null; // No filtering needed
+        const visible = new Set(allRepos.filter(r => canSeePrivateRepo(r, user)).map(r => r.name));
+        return visible;
+    }
+    const allowed = authService.getUserCollections(user.id);
+    const visible = allRepos.filter(r => canSeePrivateRepo(r, user) && (r.private && r.owner_id === user.id || allowed.includes(r.name)));
+    return new Set(visible.map(r => r.name));
+}
+function canAccessRepo(repoName, workspaceManager, getCurrentUser, authService) {
+    const user = getCurrentUser();
+    const repoConfig = workspaceManager.getRepoConfig(repoName);
+    if (!canSeePrivateRepo(repoConfig, user))
+        return false;
+    if (!user)
+        return true;
+    if (repoConfig?.private && repoConfig?.owner_id === user.id)
+        return true;
+    if (user.role === 'admin')
+        return true;
+    if (!authService)
+        return true;
+    return authService.getUserCollections(user.id).includes(repoName);
+}
+export function createGraphTools(workspaceManager, gitUser, workspacePath, onHighlight, onMutation, getCurrentUser, authService) {
+    const getUser = getCurrentUser ?? (() => null);
+    const authSvc = authService ?? null;
     return [
         // Create entity
         {
@@ -53,6 +104,9 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
                         if (!repoName)
                             return wrapToolResult({ success: false, error: `repo is required — could not auto-resolve repo for type "${params.entityType}"` });
                     }
+                    if (!canAccessRepo(repoName, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${repoName}" not found` });
+                    }
                     const graph = workspaceManager.getGraph(repoName);
                     // Workspace-level dedup: warn if an entity with this ID already exists elsewhere
                     const existing = workspaceManager.findEntityById(params.entityId);
@@ -111,6 +165,9 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
+                    if (!canAccessRepo(params.repo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.repo}" not found` });
+                    }
                     const graph = workspaceManager.getGraph(params.repo);
                     const entity = params.entityType
                         ? graph.get(params.entityType, params.entityId)
@@ -157,6 +214,9 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
                         if (!repoName)
                             return wrapToolResult({ success: false, error: `repo is required — could not auto-resolve repo for type "${params.entityType}"` });
                     }
+                    if (!canAccessRepo(repoName, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${repoName}" not found` });
+                    }
                     const graph = workspaceManager.getGraph(repoName);
                     // Add update metadata
                     const dataWithMeta = params.data
@@ -215,6 +275,9 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
                         if (!repoName)
                             return wrapToolResult({ success: false, error: `repo is required — could not auto-resolve repo for type "${params.entityType}"` });
                     }
+                    if (!canAccessRepo(repoName, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${repoName}" not found` });
+                    }
                     const graph = workspaceManager.getGraph(repoName);
                     await graph.delete(params.entityType, params.entityId, params.commitMessage);
                     onMutation?.({ action: 'deleted', repo: repoName, entityType: params.entityType, entityId: params.entityId });
@@ -245,6 +308,12 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
+                    if (!canAccessRepo(params.sourceRepo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.sourceRepo}" not found` });
+                    }
+                    if (!canAccessRepo(params.targetRepo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.targetRepo}" not found` });
+                    }
                     const sourceGraph = workspaceManager.getGraph(params.sourceRepo);
                     const targetGraph = workspaceManager.getGraph(params.targetRepo);
                     // Read the full entity from source
@@ -295,10 +364,18 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
+                    // Scope search to accessible collections
+                    const allowed = getAccessibleRepoNames(workspaceManager, getUser, authSvc);
+                    let repoNames = params.repoNames;
+                    if (allowed) {
+                        repoNames = repoNames
+                            ? repoNames.filter((r) => allowed.has(r))
+                            : [...allowed];
+                    }
                     const results = await workspaceManager.search({
                         query: params.query,
                         entityType: params.entityType,
-                        repoNames: params.repoNames,
+                        repoNames,
                         visibility: params.visibility,
                         tags: params.tags,
                         dateRange: params.dateRange,
@@ -335,7 +412,12 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
-                    const results = workspaceManager.list(params.entityType, params.limit);
+                    let results = workspaceManager.list(params.entityType, params.limit);
+                    // Filter to accessible collections
+                    const allowed = getAccessibleRepoNames(workspaceManager, getUser, authSvc);
+                    if (allowed) {
+                        results = results.filter(r => allowed.has(r.repoName));
+                    }
                     return wrapToolResult({
                         success: true,
                         count: results.length,
@@ -367,7 +449,15 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
-                    const related = workspaceManager.getRelated(params.repo, params.entityType, params.entityId);
+                    if (!canAccessRepo(params.repo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.repo}" not found` });
+                    }
+                    let related = workspaceManager.getRelated(params.repo, params.entityType, params.entityId);
+                    // Filter cross-collection results to accessible repos
+                    const allowed = getAccessibleRepoNames(workspaceManager, getUser, authSvc);
+                    if (allowed) {
+                        related = related.filter(r => allowed.has(r.repoName));
+                    }
                     return wrapToolResult({
                         success: true,
                         count: related.length,
@@ -399,7 +489,15 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
-                    const backlinks = workspaceManager.getBacklinks(params.repo, params.entityType, params.entityId);
+                    if (!canAccessRepo(params.repo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.repo}" not found` });
+                    }
+                    let backlinks = workspaceManager.getBacklinks(params.repo, params.entityType, params.entityId);
+                    // Filter cross-collection results to accessible repos
+                    const allowed = getAccessibleRepoNames(workspaceManager, getUser, authSvc);
+                    if (allowed) {
+                        backlinks = backlinks.filter(r => allowed.has(r.repoName));
+                    }
                     return wrapToolResult({
                         success: true,
                         count: backlinks.length,
@@ -431,6 +529,9 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
+                    if (!canAccessRepo(params.repo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.repo}" not found` });
+                    }
                     const validation = workspaceManager.validateWikilinks(params.repo, params.entityType, params.entityId);
                     return wrapToolResult({
                         success: true,
@@ -462,6 +563,26 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             execute: async (toolCallId, params) => {
                 try {
                     const summary = workspaceManager.getSummary();
+                    const allowed = getAccessibleRepoNames(workspaceManager, getUser, authSvc);
+                    if (allowed) {
+                        // Filter summary to accessible collections only
+                        const filteredByRepo = {};
+                        let filteredTotal = 0;
+                        for (const [repo, count] of Object.entries(summary.entitiesByRepo)) {
+                            if (allowed.has(repo)) {
+                                filteredByRepo[repo] = count;
+                                filteredTotal += count;
+                            }
+                        }
+                        return wrapToolResult({
+                            success: true,
+                            summary: {
+                                totalCollections: allowed.size,
+                                totalEntities: filteredTotal,
+                                entitiesByCollection: filteredByRepo,
+                            },
+                        });
+                    }
                     return wrapToolResult({
                         success: true,
                         summary: {
@@ -488,7 +609,11 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             parameters: T.Object({}),
             execute: async (toolCallId, params) => {
                 try {
-                    const repos = workspaceManager.getAllRepoConfigs();
+                    let repos = workspaceManager.getAllRepoConfigs();
+                    const allowed = getAccessibleRepoNames(workspaceManager, getUser, authSvc);
+                    if (allowed) {
+                        repos = repos.filter(r => allowed.has(r.name));
+                    }
                     return wrapToolResult({
                         success: true,
                         count: repos.length,
@@ -513,13 +638,19 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
         {
             name: 'create_collection',
             label: 'Create Collection',
-            description: 'Create a new collection in the workspace. A collection is a git-backed container for entities.',
+            description: 'Create a new collection in the workspace. A collection is a git-backed container for entities. Private collections are only visible to the creating user.',
             parameters: T.Object({
                 name: T.String({ description: 'Collection name in kebab-case (e.g., "client-projects")' }),
                 description: T.Optional(T.String({ description: 'Short description of the collection' })),
+                private: T.Optional(T.Boolean({ description: 'If true, creates a private collection visible only to you' })),
             }),
             execute: async (toolCallId, params) => {
                 try {
+                    const user = getUser();
+                    // Non-private collections require admin; private collections can be created by anyone
+                    if (!params.private && user && user.role !== 'admin') {
+                        return wrapToolResult({ success: false, error: 'Only admins can create collections' });
+                    }
                     if (!/^[a-z0-9][a-z0-9-]*$/.test(params.name)) {
                         return wrapToolResult({ success: false, error: 'Collection name must be kebab-case (lowercase letters, numbers, hyphens)' });
                     }
@@ -528,6 +659,8 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
                     const repo = await workspace.registerRepo({
                         name: params.name,
                         description: params.description,
+                        private: params.private,
+                        ...(params.private && user ? { owner_id: user.id } : {}),
                     });
                     // Reload workspace manager to pick up the new collection
                     workspaceManager.reloadConfig();
@@ -555,6 +688,9 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
+                    if (!canAccessRepo(params.repo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.repo}" not found` });
+                    }
                     const graph = workspaceManager.getGraph(params.repo);
                     const entity = graph.get('dataset', params.entityId);
                     const schema = entity.data.schema;
@@ -591,6 +727,9 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
+                    if (!canAccessRepo(params.repo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.repo}" not found` });
+                    }
                     const graph = workspaceManager.getGraph(params.repo);
                     // Get current row count before appending
                     const beforeRows = graph.getDatasetRows(params.entityId);
@@ -664,10 +803,17 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
-                    const issues = await lintWorkspace(workspaceManager, {
+                    if (params.repo && !canAccessRepo(params.repo, workspaceManager, getUser, authSvc)) {
+                        return wrapToolResult({ success: false, error: `Collection "${params.repo}" not found` });
+                    }
+                    let issues = await lintWorkspace(workspaceManager, {
                         repo: params.repo,
                         entityType: params.entityType,
                     });
+                    const allowed = getAccessibleRepoNames(workspaceManager, getUser, authSvc);
+                    if (allowed) {
+                        issues = issues.filter(i => allowed.has(i.repo));
+                    }
                     // Group by entity type for easier reading
                     const grouped = new Map();
                     for (const issue of issues) {
@@ -713,10 +859,16 @@ export function createGraphTools(workspaceManager, gitUser, workspacePath, onHig
             }),
             execute: async (toolCallId, params) => {
                 try {
+                    // Scope to accessible collections
+                    const allowed = getAccessibleRepoNames(workspaceManager, getUser, authSvc);
+                    let repos = params.repos;
+                    if (allowed) {
+                        repos = repos ? repos.filter((r) => allowed.has(r)) : [...allowed];
+                    }
                     const result = findOrphans(workspaceManager, {
                         entityTypes: params.entityTypes,
                         minAgeDays: params.minAgeDays,
-                        repos: params.repos,
+                        repos,
                     });
                     // Tombstone if requested
                     if (params.tombstone && workspacePath && result.orphans.length > 0) {