studiograph 1.3.46 → 1.3.48-beta.0

package/dist/core/workspace.js

@@ -5,9 +5,11 @@
  * Similar to how Git works with .git/
  */
 import { appendFileSync, existsSync, mkdirSync, readFileSync, readdirSync, statSync, writeFileSync } from 'fs';
-import { execSync, spawnSync } from 'child_process';
+import { execFileSync, spawnSync } from 'child_process';
 import { join } from 'path';
 import { setUserModelConfig } from './user-config.js';
+import { enforceWorkspaceConfig } from './schemas/workspace.js';
+import { sanitize } from '../server/middleware/sanitize.js';
 export class Workspace {
     workspacePath;
     jsonConfigPath;
@@ -53,7 +55,8 @@ export class Workspace {
         writeFileSync(this.membersPath, JSON.stringify(initialMembers, null, 2), 'utf-8');
         // Create .gitignore for .studiograph
         const gitignorePath = join(studiographDir, '.gitignore');
-        writeFileSync(gitignorePath, '# Ignore sensitive local config\n*.local\nauth.db\nauth.db-wal\nauth.db-shm\nauth-secret\napi-keys\n');
+        writeFileSync(gitignorePath, '# Ignore sensitive local config\n*.local\nauth.db\nauth.db-wal\nauth.db-shm\nauth-secret\napi-keys\n' +
+            '# Yjs binary snapshot state (per-instance, not git-friendly)\nyjs-state/\n');
         // Create scaffolded ABOUT.md
         this.writeAbout('## Vision\n\n## Mission\n\n## Profile\n\n## Capabilities\n\n## Values\n');
     }
@@ -72,10 +75,44 @@ export class Workspace {
         return this.config;
     }
     /**
-     * Write workspace config as workspace.json
+     * Write workspace config as workspace.json.
+     *
+     * Phase 5 dual-write: the R2 credential fields
+     * (`r2_config.access_key_id`, `r2_config.secret_access_key`) and the
+     * search api_key are mirrored into the encrypted store (when the
+     * store has been initialized). Failures never block the file write.
+     *
+     * Phase 9c: every write goes through `enforceWorkspaceConfig`, which
+     * throws `SchemaViolationError` when `STUDIOGRAPH_SCHEMA_STRICT` is on
+     * (default) and the validator finds a secret-shaped field, or falls
+     * back to warn-mode logging when the env is `'0'`. The throw blocks
+     * the write — workspace.json is committed and must never carry
+     * literals.
      */
     writeConfig(config) {
+        // Phase 9c: strict-or-warn schema enforcement. In strict mode (the
+        // default), violations throw and abort the write; callers translate
+        // into HTTP 400 (config-api) or CLI exit 1 (sync/clone/join). In
+        // warn-mode fallback (`STUDIOGRAPH_SCHEMA_STRICT=0`) the previous
+        // log-only behaviour is preserved for hotfix.
+        enforceWorkspaceConfig(config);
         writeFileSync(this.jsonConfigPath, JSON.stringify(config, null, 2), 'utf-8');
+        void this._dualWrite(config);
+    }
+    /**
+     * Lazy import of the dual-write helper. Best-effort — `mirrorWorkspaceConfig`
+     * itself short-circuits when the store hasn't been initialized
+     * (e.g. very early boot, tests without a store). Failures log + swallow.
+     */
+    async _dualWrite(config) {
+        try {
+            const { mirrorWorkspaceConfig } = await import('./secrets/dual-write.js');
+            await mirrorWorkspaceConfig(config);
+        }
+        catch (err) {
+            // eslint-disable-next-line no-console
+            console.warn(`[secrets] dual-write workspace.json mirror failed: ${err instanceof Error ? err.message : String(err)}`);
+        }
     }
     /**
      * Commit workspace.json and push to the config repo remote (if one exists).
@@ -109,18 +146,20 @@ export class Workspace {
                 'commit', '-m', message,
             ], { cwd: sgDir, encoding: 'utf-8', stdio: 'pipe' });
             if (commit.status !== 0) {
-                console.warn(`Workspace: failed to commit workspace.json — ${(commit.stderr || '').trim()}`);
+                // Phase 11: git stderr can echo remote URL credentials on
+                // failure — route through sanitize() before logging.
+                console.warn(`Workspace: failed to commit workspace.json — ${sanitize((commit.stderr || '').trim())}`);
                 return;
             }
             const push = spawnSync('git', ['push'], {
                 cwd: sgDir, encoding: 'utf-8', stdio: 'pipe', timeout: 30_000,
             });
             if (push.status !== 0) {
-                console.warn(`Workspace: failed to push workspace.json — ${(push.stderr || '').trim()}`);
+                console.warn(`Workspace: failed to push workspace.json — ${sanitize((push.stderr || '').trim())}`);
             }
         }
         catch (err) {
-            console.warn(`Workspace: config sync failed — ${err.message}`);
+            console.warn(`Workspace: config sync failed — ${sanitize(err.message)}`);
         }
     }
     /**
@@ -167,19 +206,6 @@ export class Workspace {
     setModelConfig(provider, modelId, apiKey) {
         setUserModelConfig(provider, modelId, apiKey);
     }
-    /**
-     * Generate README content for a repo
-     */
-    generateRepoReadme(repo) {
-        return `# ${repo.name}
-
-${repo.description || 'No description provided.'}
-
-This collection is part of a Studiograph workspace. Entities are stored as markdown files with YAML frontmatter in type subfolders (e.g. \`meetings/\`, \`decisions/\`).
-
-Use \`[[wikilinks]]\` to link entities across collections.
-`;
-    }
     /**
      * Register a new repo in the workspace
      */
@@ -189,22 +215,31 @@ Use \`[[wikilinks]]\` to link entities across collections.
         if (config.repos.find(r => r.name === repo.name)) {
             throw new Error(`Repo '${repo.name}' already registered`);
         }
+        // Each user can have at most one personal folder
+        if (repo.personal && repo.owner_id != null) {
+            const existing = config.repos.find(r => r.personal === true && r.owner_id === repo.owner_id);
+            if (existing) {
+                throw new Error(`User ${repo.owner_id} already has a personal folder '${existing.name}'`);
+            }
+        }
         // Create repo config with path
         const repoConfig = {
             ...repo,
             path: repo.name, // Path relative to workspace root
-            ...(repo.private ? { private: true } : {}),
+            ...(repo.personal ? { personal: true } : {}),
         };
         // Add to config
         config.repos.push(repoConfig);
         this.writeConfig(config);
         this.config = config;
-        this.pushWorkspaceConfig(`Add collection: ${repo.name}`);
+        this.pushWorkspaceConfig(`Add folder: ${repo.name}`);
         // Create repo directory
         const repoPath = join(this.workspacePath, repo.name);
         mkdirSync(repoPath, { recursive: true });
-        if (repo.private) {
-            // Private collections: add to workspace .gitignore, no marker or README
+        if (repo.personal) {
+            // Personal folders: add to workspace .gitignore, no marker.
+            // The folder lives outside the team git workspace; if shared later via
+            // folder_access, it still stays out of the team repo.
             const wsGitignore = join(this.workspacePath, '.gitignore');
             const entry = `${repo.name}/`;
             if (existsSync(wsGitignore)) {
@@ -218,25 +253,24 @@ Use \`[[wikilinks]]\` to link entities across collections.
             }
         }
         else {
-            // Public collections: marker, README, git init
+            // Team folders: drop a .studiograph marker so other tools can detect
+            // that the directory is a workspace repo. (No README — see commit
+            // history; auto-generated READMEs added more cleanup churn than value.)
             const repoMarkerPath = join(repoPath, '.studiograph');
             writeFileSync(repoMarkerPath, JSON.stringify({ repo_name: repo.name }, null, 2), 'utf-8');
-            const readmePath = join(repoPath, 'README.md');
-            const readmeContent = this.generateRepoReadme(repoConfig);
-            writeFileSync(readmePath, readmeContent, 'utf-8');
         }
         // Initialize git repo with .gitignore and initial commit
         const gitDir = join(repoPath, '.git');
         if (!existsSync(gitDir)) {
-            const run = (cmd) => execSync(cmd, { cwd: repoPath, stdio: 'pipe' });
-            run('git init');
-            run('git branch -M main');
+            const run = (args) => execFileSync('git', args, { cwd: repoPath, stdio: 'pipe' });
+            run(['init']);
+            run(['branch', '-M', 'main']);
             const gitignorePath = join(repoPath, '.gitignore');
             if (!existsSync(gitignorePath)) {
                 writeFileSync(gitignorePath, '.DS_Store\n*.tmp\n*.log\n', 'utf-8');
             }
-            run('git add -A');
-            run('git -c user.name="Studiograph" -c user.email="noreply@studiograph.dev" commit -m "Initialize repo"');
+            run(['add', '-A']);
+            run(['-c', 'user.name=Studiograph', '-c', 'user.email=noreply@studiograph.dev', 'commit', '-m', 'Initialize repo']);
         }
         return repoConfig;
     }
@@ -279,11 +313,11 @@ Use \`[[wikilinks]]\` to link entities across collections.
         for (const entry of entries) {
             if (!entry.isDirectory())
                 continue;
-            // Skip hidden dirs, .studiograph config dir, and private collections
+            // Skip hidden dirs, .studiograph config dir, and personal folders
             if (entry.name.startsWith('.'))
                 continue;
-            const isPrivateDir = config.repos.some(r => r.path === entry.name && r.private);
-            if (isPrivateDir)
+            const isPersonalDir = config.repos.some(r => r.path === entry.name && r.personal);
+            if (isPersonalDir)
                 continue;
             const dirPath = join(this.workspacePath, entry.name);
             const markerPath = join(dirPath, '.studiograph');

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package/dist/mcp/comment-virtual-entity.d.ts

@@ -0,0 +1,36 @@
+import type { CommentService } from '../services/comment-service.js';
+/**
+ * Comments live in SQLite for throughput, but agents should see them as
+ * first-class typed entities just like notes, projects, etc. This adapter
+ * shapes a Comment row into the same `{ id, entityType, data, content }`
+ * envelope that file-backed entities use, so generic MCP tools (`get_entity`,
+ * `list_entities`, `find_related`) can return comments without per-type
+ * branches in the tool code itself.
+ *
+ * The shape mirrors what `wm.getGraph(repo).get(...)` returns from
+ * filesystem entities: `id` is the comment_id (used in MCP URIs), `entityType`
+ * is the literal ‘comment’, `data` is frontmatter-flat with comment metadata,
+ * and `content` is the comment body.
+ */
+export interface VirtualEntityEnvelope {
+    id: string;
+    entityType: 'comment';
+    data: Record<string, unknown>;
+    document: {
+        content: string;
+        wikilinks: string[];
+    };
+}
+export declare function getComment(commentService: CommentService, commentId: string): VirtualEntityEnvelope | null;
+export declare function listComments(commentService: CommentService, opts?: {
+    repo?: string;
+    entryType?: string;
+    entryId?: string;
+    resolved?: boolean;
+    limit?: number;
+}): VirtualEntityEnvelope[];
+/**
+ * Comments anchored to a given entry — exposed as backlinks of that entry
+ * so `find_related` includes them naturally.
+ */
+export declare function findRelatedComments(commentService: CommentService, repo: string, entityType: string, entityId: string): VirtualEntityEnvelope[];

package/dist/mcp/comment-virtual-entity.js

@@ -0,0 +1,71 @@
+import { parseCellAnchor } from '../core/cell-anchor.js';
+function toEnvelope(c) {
+    // For dataset cell comments the anchor is JSON in anchor_relpos — surface
+    // the column + row snapshot so an agent reading the comment as an entity can
+    // locate the cell, not just see the bare cell value.
+    const cell = parseCellAnchor(c.anchorRelpos);
+    return {
+        id: c.commentId,
+        entityType: 'comment',
+        data: {
+            entity_type: 'comment',
+            entity_id: c.commentId,
+            created_at: c.createdAt,
+            updated_at: c.updatedAt ?? c.createdAt,
+            created_by: c.authorDisplayName,
+            updated_by: c.authorDisplayName,
+            // Comment-specific fields. Naming matches the SQL schema for
+            // consistency with the public REST API.
+            repo: c.repo,
+            entry_type: c.entryType,
+            entry_id: c.entryId,
+            thread_id: c.threadId,
+            parent_id: c.parentId,
+            author_user_id: c.authorUserId,
+            author_role: c.authorRole,
+            anchor_quote: c.anchorQuote,
+            ...(cell
+                ? {
+                    anchor_cell: {
+                        column: cell.headerName,
+                        column_index: cell.columnIndex,
+                        ...(cell.rowCells ? { row_cells: cell.rowCells } : {}),
+                    },
+                }
+                : {}),
+            resolved_at: c.resolvedAt,
+            resolved_by_user_id: c.resolvedByUserId,
+            edited: c.edited === 1,
+            mentions: c.mentions.map(m => m.handle),
+        },
+        document: { content: c.body, wikilinks: extractWikilinks(c.body) },
+    };
+}
+const WIKILINK_RE = /\[\[([^\]|#]+)(?:\|[^\]]+)?\]\]/g;
+function extractWikilinks(body) {
+    const out = [];
+    for (const match of body.matchAll(WIKILINK_RE)) {
+        if (match[1])
+            out.push(match[1].trim());
+    }
+    return out;
+}
+export function getComment(commentService, commentId) {
+    const c = commentService.getById(commentId);
+    if (!c || c.deletedAt)
+        return null;
+    return toEnvelope(c);
+}
+export function listComments(commentService, opts = {}) {
+    return commentService.list(opts).map(toEnvelope);
+}
+/**
+ * Comments anchored to a given entry — exposed as backlinks of that entry
+ * so `find_related` includes them naturally.
+ */
+export function findRelatedComments(commentService, repo, entityType, entityId) {
+    return commentService
+        .list({ repo, entryType: entityType, entryId: entityId })
+        .map(toEnvelope);
+}
+//# sourceMappingURL=comment-virtual-entity.js.map

package/dist/mcp/comment-virtual-entity.js.map

@@ -0,0 +1 @@
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package/dist/mcp/connector-manager.d.ts

@@ -4,8 +4,9 @@
  * Connects the Studiograph agent to third-party MCP servers so the agent can
  * query external data sources on demand.
  *
- * Only HTTP transport is supported (Streamable HTTP). Connectors are configured
- * with a URL and optional headers — same format as Cursor/Claude Code MCP configs.
+ * Supports two transports:
+ *   - HTTP (Streamable HTTP) — `url` + optional `headers`
+ *   - Stdio — `command` + `args` + optional `env`
  *
  * Two-layer config:
  *
@@ -22,6 +23,8 @@
  *
  * Connection failures are non-fatal — the failing connector is skipped with a warning.
  */
+import type { OAuthClientProvider } from '@modelcontextprotocol/sdk/client/auth.js';
+import type { AuthService } from '../services/auth-service.js';
 export declare const CONNECTORS_DIR: string;
 export interface ConnectorConfig {
     /** Unique name used as the tool prefix (e.g. "linear" → "linear__search_issues") */
@@ -32,24 +35,40 @@ export interface ConnectorConfig {
     headers?: Record<string, string>;
     /** Human-readable description shown in tool labels */
     description?: string;
-    /** Auth mode: 'oauth' uses per-user OAuth tokens, 'headers' uses manual headers, 'none' for local connectors */
-    auth?: 'headers' | 'oauth' | 'none';
+    /** Pre-registered OAuth app credentials (for servers that don't support dynamic registration) */
+    oauth?: {
+        client_id: string;
+        client_secret?: string;
+    };
+    /** Auto-detected: server advertises OAuth support via .well-known */
+    requiresOAuth?: boolean;
 }
-export declare const KNOWN_CONNECTORS: Record<string, import("../integrations/types.js").ConnectorSpec>;
 export declare class ConnectorManager {
     /**
      * Load all connector configs, merging workspace + homedir layers.
-     * When workspacePath is provided, reads .studiograph/connectors/ first,
-     * then overlays homedir configs (homedir fields win).
      */
     static loadConfigs(workspacePath?: string): ConnectorConfig[];
     /**
      * Load connector configs from workspace .studiograph/connectors/ only.
-     * Used by the config bundle export endpoint.
      */
     static loadWorkspaceConfigs(workspacePath: string): ConnectorConfig[];
-    /** Save full config to homedir (mode 0600, never committed). */
+    /**
+     * Save full config to homedir (mode 0600, never committed).
+     *
+     * Phase 5 dual-write: when the encrypted store has been initialized,
+     * the connector's secret-bearing fields (`headers.Authorization`,
+     * `oauth.client_secret`) are mirrored into the store under
+     * workspace-scope keys (`connector.<name>.auth`,
+     * `connector.<name>.oauth_secret`). Failures never block the file
+     * write — see dual-write.ts. The legacy file remains authoritative
+     * through Phase 5; Phase 6 flipped the read path.
+     */
     static saveConfig(config: ConnectorConfig): void;
+    /**
+     * Lazy import of the dual-write helper so the secrets store is only
+     * loaded when the flag is on. Best-effort — failures log + swallow.
+     */
+    private static _dualWrite;
     /** Save sanitized config to workspace .studiograph/connectors/ (git-tracked). */
     static saveWorkspaceConfig(config: ConnectorConfig, workspacePath: string): void;
     static removeConfig(name: string, workspacePath?: string): boolean;
@@ -62,16 +81,78 @@ export declare class ConnectorManager {
     static stripSecrets(config: ConnectorConfig): ConnectorConfig;
     /** Expands $ENV_VAR references; returns the literal string otherwise. */
     static resolveEnvVar(value: string): string;
+    /**
+     * Parse a JSON config block into ConnectorConfig(s).
+     * Supports three formats:
+     *   A) Single server: { command, args, env } or { url, headers }
+     *   B) Named servers: { mcpServers: { name: { ... } } }
+     *   C) Single named: { name: "...", command/url: "..." }
+     */
+    static parseConfigBlock(json: string, defaultName?: string): ConnectorConfig[];
+    private static _normalizeServerConfig;
+    /** Try to infer a connector name from the URL. */
+    private static _inferName;
     /**
      * For each connector config: connect to the MCP server, fetch its tool list,
-     * and return Pi-Mono-compatible tool objects with namespaced names.
+     * and return tool objects with namespaced names.
+     *
+     * Auth precedence (single rule across the codebase):
+     *   1. Per-user OAuth tokens (when `opts.userId` + `opts.authService` resolve
+     *      `hasOAuthTokens === true`) — restores the original `McpOAuthProvider`
+     *      design intent: tokens stored per `(user, connector)` are actually
+     *      *used* upstream. The provider's `tokens()` returns the user's row;
+     *      the SDK refreshes via `saveTokens` writing back to the same row.
+     *   2. Workspace static `Authorization` header (`config.headers.Authorization`)
+     *      — admin-configured shared identity. Used when the caller has no user
+     *      session (CLI, MCP server, agent pool spawned without `userId`) or
+     *      when the user hasn't bound their own OAuth credential yet.
+     *   3. Skip — `requiresOAuth` connector with neither per-user OAuth nor a
+     *      workspace header has no usable credential.
      *
      * Failures are non-fatal — the connector is skipped with a console.warn.
      */
-    static buildTools(configs: ConnectorConfig[], timeoutMs?: number): Promise<any[]>;
-    /** Read all valid connector configs from a directory. */
+    static buildTools(configs: ConnectorConfig[], opts?: {
+        userId?: number;
+        authService?: AuthService;
+        /** Studiograph server URL — only consulted if a refresh fails and the SDK
+         *  initiates a re-auth flow (which the runtime can't complete anyway —
+         *  we surface a 401 to the UI instead). Safe to pass an empty string. */
+        serverUrl?: string;
+        timeoutMs?: number;
+    }): Promise<any[]>;
+    /**
+     * Decide which credential to use for a connector. Public so the precedence
+     * rule can be unit-tested without spinning up a real MCP server.
+     *
+     * Returns one of:
+     *   - `{ mode: 'user-oauth', authProvider }`: per-user OAuth tokens win. The
+     *     transport will read tokens via the provider's `tokens()` and refresh
+     *     back to the user's row.
+     *   - `{ mode: 'workspace-header' }`: the workspace static `Authorization`
+     *     header is used. The transport gets the header directly; the OAuth
+     *     machinery is not touched.
+     *   - `{ mode: 'skip-placeholder' }`: the workspace header contains an
+     *     unresolved `$ENV_VAR` placeholder — nothing usable, skip silently.
+     *   - `{ mode: 'skip-no-credential' }`: connector requires OAuth but has
+     *     neither per-user tokens nor a workspace header.
+     */
+    static resolveConnectorAuth(config: ConnectorConfig, opts?: {
+        userId?: number;
+        authService?: AuthService;
+        serverUrl?: string;
+    }): {
+        mode: 'user-oauth';
+        authProvider: OAuthClientProvider;
+    } | {
+        mode: 'workspace-header';
+    } | {
+        mode: 'skip-placeholder';
+    } | {
+        mode: 'skip-no-credential';
+    };
+    /** Resolve OAuth credentials from a connector config or fall back to broker. */
+    private static _resolveOAuthCredentials;
     private static _readDir;
-    /** Merge two configs for the same connector — overlay fields win over base. */
     private static _merge;
     private static _validate;
     private static _buildConnectorTools;