studiograph 1.3.47 → 1.3.48-beta.1

package/dist/cli/commands/serve.js

@@ -13,7 +13,8 @@
  */
 import { Command } from 'commander';
 import { join } from 'path';
-import { exec } from 'child_process';
+import { homedir } from 'os';
+import { exec, spawnSync } from 'child_process';
 import { existsSync } from 'fs';
 import { Workspace } from '../../core/workspace.js';
 import { WorkspaceManager } from '../../core/workspace-manager.js';
@@ -23,6 +24,12 @@ import { runPreflight } from '../../utils/preflight.js';
 import { createServer } from '../../server/index.js';
 import { box } from 'consola/utils';
 import { header, dimText } from '../colors.js';
+import { SqliteEncryptedStore, loadMasterKey, loadPreviousMasterKey, setSecretStore, } from '../../core/secrets/index.js';
+import { tryResolve } from '../../core/secrets/read-flip.js';
+import { migrateAuthDbPhase8 } from '../../core/secrets/auth-db-migration.js';
+import { migrateR2Structural } from '../../core/secrets/r2-structural-migration.js';
+import { installConsolePatch } from '../../utils/log.js';
+import { incrementalReindexWorkspace } from '../../services/vector-service.js';
 export const serveCommand = new Command('serve')
     .description('Start the Studiograph HTTP server')
     .option('-p, --port <port>', 'Port to listen on', '8000')
@@ -37,6 +44,16 @@ export const serveCommand = new Command('serve')
     if (process.env.RAILWAY_ENVIRONMENT && existsSync('/workspace')) {
         process.chdir('/workspace');
     }
+    // Ensure git operations work regardless of file ownership. The workspace
+    // volume may have files owned by a different uid than the running process
+    // (e.g. after container restart or data import), which triggers git's
+    // "dubious ownership" refusal. Without this, the embedded git HTTP server
+    // returns empty refs for cloned folders. Docker entrypoint does this
+    // too, but Railway bypasses the entrypoint via `npx` start command.
+    try {
+        spawnSync('git', ['config', '--global', '--add', 'safe.directory', '*'], { stdio: 'ignore' });
+    }
+    catch { /* non-fatal */ }
     const workspace = new Workspace();
     if (!workspace.isWorkspace()) {
         console.error('Not a Studiograph workspace. Run `studiograph init` first.');
@@ -47,7 +64,115 @@ export const serveCommand = new Command('serve')
         process.exit(1);
         return;
     }
+    // Phase 11: install the production console patch as soon as we know
+    // the master key is loaded. Patches console.log/info/warn/error/debug
+    // so any direct console call (third-party, yet-to-migrate, or
+    // unexpected) flows through sanitize() before reaching stdout in
+    // production. No-op outside production unless RAILWAY_ENVIRONMENT
+    // is set. Honours STUDIOGRAPH_LOG_RAW=1 as an escape hatch.
+    //
+    // Installed BEFORE the secrets-store messages below so the redactor
+    // is live by the time we log the master-key source. The master-key
+    // source itself is a friendly label ('env'/'file'/'first-run'), not
+    // a secret, so the line passes through unredacted in practice.
+    //
+    // The encrypted secrets store + Phase 8 auth.db migration + first-run
+    // importer all run unconditionally. The `STUDIOGRAPH_NEW_STORE` env
+    // flag that previously gated this block was removed once Phase 6
+    // shipped stably in production; setting the var is now a no-op.
+    let authCryptoOptions;
+    try {
+        const loaded = loadMasterKey();
+        const previous = loadPreviousMasterKey();
+        installConsolePatch();
+        const sgRoot = process.env.RAILWAY_ENVIRONMENT && existsSync('/workspace')
+            ? '/workspace'
+            : join(homedir(), '.studiograph');
+        const dbPath = join(sgRoot, 'secrets.db');
+        const store = new SqliteEncryptedStore({
+            dbPath,
+            masterKey: loaded.key,
+            previousMasterKey: previous,
+        });
+        setSecretStore(store);
+        console.log(`[secrets] store ready at ${dbPath} (master key from ${loaded.source})`);
+        // Stash the master key so AuthService (constructed later in
+        // createServer) can use it for per-user OAuth + settings encryption.
+        authCryptoOptions = { masterKey: loaded.key };
+        // Phase 8: auth.db column upgrades. Runs BEFORE the importer
+        // (defensive ordering — even though today's importer doesn't
+        // touch user-secret keys, a future importer could mirror
+        // auth.db values into the store and would need the new schema
+        // already in place). Idempotent — re-running after success is
+        // a no-op via meta.auth_db_phase8_migrated_at. Failure is fatal:
+        // a half-rebuilt oauth_tokens would corrupt OAuth flows for
+        // every MCP connector, so refusing to start is safer than
+        // serving with mixed plaintext/ciphertext rows.
+        try {
+            const authDbPath = join(process.cwd(), '.studiograph', 'auth.db');
+            const migrationResult = migrateAuthDbPhase8({
+                authDbPath,
+                masterKey: loaded.key,
+            });
+            if (!migrationResult.skipped) {
+                console.log(`[secrets] Encrypted per-user secrets (one-time migration): ` +
+                    `${migrationResult.oauthRowsMigrated} oauth_tokens row(s), ` +
+                    `${migrationResult.prefsRowsMigrated} user_preferences row(s). ` +
+                    `Backup at ${migrationResult.backupPath}.`);
+            }
+        }
+        catch (err) {
+            console.error('[secrets] auth.db Phase 8 migration failed; refusing to start:', err instanceof Error ? err.message : err);
+            process.exit(1);
+        }
+        // Phase 12 decommission (2026-05-12): the first-run importer that
+        // copied legacy ~/.studiograph/user.json + connectors/*.json +
+        // workspace.json fields into the store ran successfully on every
+        // existing workspace. With no migration ramp left to support,
+        // operators write values via the Settings UI or `studiograph
+        // secrets set` CLI directly.
+        // Post-Phase-12 one-shot: copy the four R2 structural fields
+        // (account_id, bucket, public_url, endpoint) from
+        // workspace.json:r2_config.* into the store on first encounter.
+        // The credentials (access_key_id / secret_access_key) were already
+        // store-resident; this fills the structural gap so the Settings UI
+        // can fully configure R2 without anyone touching the file. Marker
+        // gates re-runs. Non-fatal — see migrateR2Structural's doc.
+        try {
+            const workspaceJsonPath = join(process.cwd(), '.studiograph', 'workspace.json');
+            const r2Result = await migrateR2Structural({ workspaceJsonPath, store });
+            if (!r2Result.skipped && r2Result.written.length > 0) {
+                console.log(`[secrets] Imported R2 structural fields from workspace.json: ${r2Result.written.join(', ')}`);
+            }
+        }
+        catch (err) {
+            console.warn('[secrets] R2 structural migration failed (non-fatal):', err instanceof Error ? err.message : err);
+        }
+    }
+    catch (err) {
+        // Hard error — the store is required to boot. A misconfigured
+        // master key or unreadable secrets.db should surface immediately
+        // rather than silently fall back.
+        console.error('[secrets] failed to initialize store:', err instanceof Error ? err.message : err);
+        process.exit(1);
+    }
     const config = await workspace.loadConfig();
+    // Configure each folder repo to accept pushes to the checked-out branch.
+    // By default, git refuses `git push` into a non-bare repo's checked-out branch
+    // because it desyncs the working tree. `updateInstead` accepts pushes that
+    // fast-forward AND keeps the working tree in sync, which is exactly what we
+    // want for folder data pushed via `studiograph push --remote --data` → the
+    // embedded git HTTP server. Without this, the git receive-pack rejects with
+    // "branch is currently checked out."
+    for (const repo of config.repos) {
+        const repoGit = join(process.cwd(), repo.path, '.git');
+        if (!existsSync(repoGit))
+            continue;
+        try {
+            spawnSync('git', ['-C', join(process.cwd(), repo.path), 'config', 'receive.denyCurrentBranch', 'updateInstead'], { stdio: 'ignore' });
+        }
+        catch { /* non-fatal */ }
+    }
     // Prompt for model setup if not configured (non-blocking — server works without it, but chat won't)
     await promptLLMSetupIfNeeded();
     // Propagate API key from user config to env (orchestrator reads provider env vars)
@@ -61,26 +186,62 @@ export const serveCommand = new Command('serve')
         email: 'noreply@studiograph.local',
     };
     const workspaceManager = new WorkspaceManager(process.cwd(), config, gitUser);
-    // Read API keys: workspace-managed key + any from environment
-    const { AuthService } = await import('../../services/auth-service.js');
-    const authService = new AuthService(process.cwd());
-    const managedKey = authService.getApiKey();
-    authService.close();
-    const apiKeysEnv = process.env.API_KEYS || '';
-    const envKeys = apiKeysEnv.split(';').map(k => k.trim()).filter(k => k.length > 0);
-    const apiKeys = [managedKey, ...envKeys.filter(k => k !== managedKey)];
+    // Auto-index on boot. Replaces the auto-index that used to live in
+    // `studiograph start` (deleted in Phase C). Non-fatal — a failed index
+    // shouldn't keep the workspace from serving.
+    const autoOnBoot = tryResolve('index.auto_on_boot') ?? true;
+    if (autoOnBoot) {
+        try {
+            // First-time index renders a single-line progress bar in TTY
+            // sessions. Voyage batches at 128/request, so each callback
+            // tick is a real chunk of remote work — no need to throttle the
+            // re-render. In non-TTY environments (CI, Railway, piped),
+            // suppress the bar entirely so the log stays line-oriented.
+            const isTTY = !!process.stdout.isTTY;
+            let progressStarted = false;
+            const renderProgress = (done, total) => {
+                if (!isTTY || total === 0)
+                    return;
+                if (!progressStarted) {
+                    process.stdout.write('[index] first-run indexing — this can take a few minutes the first time\n');
+                    progressStarted = true;
+                }
+                const width = 28;
+                const ratio = Math.min(1, done / total);
+                const filled = Math.round(ratio * width);
+                const bar = '█'.repeat(filled) + '░'.repeat(width - filled);
+                const pct = Math.round(ratio * 100).toString().padStart(3);
+                process.stdout.write(`\r[index] ${bar} ${pct}% (${done}/${total})`);
+            };
+            const result = await incrementalReindexWorkspace(workspaceManager, config.repos, process.cwd(), {
+                log: (msg) => console.warn(`[index] ${msg}`),
+                onFirstTimeProgress: renderProgress,
+            });
+            if (progressStarted) {
+                // Close out the progress line so the next log starts on a fresh line.
+                process.stdout.write('\n');
+            }
+            if (result.fresh) {
+                console.log(`[index] first-run index complete: ${result.total} entit${result.total === 1 ? 'y' : 'ies'}`);
+            }
+            else if (result.total > 0) {
+                console.log(`[index] incremental update: ${result.total} entit${result.total === 1 ? 'y' : 'ies'} reindexed`);
+            }
+        }
+        catch (err) {
+            console.warn('[index] auto-index on boot failed (non-fatal):', err instanceof Error ? err.message : err);
+        }
+    }
     const port = parseInt(process.env.PORT || opts.port, 10);
     const host = process.env.HOST || opts.host;
-    const appsDir = join(process.cwd(), '.studiograph', 'apps');
     const server = await createServer({
         workspaceManager,
         workspacePath: process.cwd(),
         workspaceConfig: config,
         gitUser,
-        appsDir,
         port,
         host,
-        apiKeys,
+        authCryptoOptions,
     });
     // Try to listen, auto-incrementing port if in use
     let actualPort = port;
@@ -99,12 +260,12 @@ export const serveCommand = new Command('serve')
             process.exit(1);
         }
     }
-    const collections = config.repos.length;
+    const folders = config.repos.length;
     const hasChat = !!llmApiKey;
     const url = `http://localhost:${actualPort}`;
     console.log(box([
         `URL:          ${header(url)}`,
-        `Collections:  ${collections}`,
+        `Folders:      ${folders}`,
         `Chat:         ${hasChat ? 'enabled' : dimText('disabled (run studiograph config to add an AI model)')}`,
     ].join('\n'), {
         title: `Studiograph — ${config.team_name}`,
@@ -119,20 +280,44 @@ export const serveCommand = new Command('serve')
         exec(`${openUrl} ${url}`);
     }
     console.log(dimText('Press Ctrl+C to stop the server.\n'));
-    // Graceful shutdown
-    const shutdown = async (signal) => {
+    // Graceful shutdown. server.close() runs the onClose hook which
+    // awaits sessionManager.shutdown() — flushing pending commits BEFORE
+    // tearing down the timer. The 10s force-exit budget lets larger flushes
+    // complete; SessionManager also persists to disk on every markDirty
+    // so the next boot's recoverOnBoot() catches anything that doesn't
+    // make it out before the timeout fires.
+    let shuttingDown = false;
+    const shutdown = async (signal, exitCode) => {
+        if (shuttingDown)
+            return;
+        shuttingDown = true;
         console.log(`[serve] ${signal} received — shutting down gracefully`);
-        // Force exit after 5s if server.close() hangs on open connections
         const forceTimer = setTimeout(() => {
             console.log('[serve] forcing exit after timeout');
-            process.exit(0);
-        }, 5000);
+            process.exit(exitCode);
+        }, 10000);
         forceTimer.unref();
-        await server.close();
-        console.log(`[serve] shutdown complete`);
-        process.exit(0);
+        try {
+            await server.close();
+            console.log(`[serve] shutdown complete`);
+        }
+        catch (err) {
+            console.error('[serve] shutdown error:', err);
+        }
+        process.exit(exitCode);
     };
-    process.once('SIGTERM', () => shutdown('SIGTERM'));
-    process.once('SIGINT', () => shutdown('SIGINT'));
+    process.once('SIGTERM', () => shutdown('SIGTERM', 0));
+    process.once('SIGINT', () => shutdown('SIGINT', 0));
+    // Crash handlers — last-chance flush. Pending sessions are already
+    // persisted on every markDirty/flush, so recoverOnBoot() recovers
+    // anything that doesn't make it out here.
+    process.on('uncaughtException', (err) => {
+        console.error('[serve] uncaughtException:', err);
+        shutdown('uncaughtException', 1);
+    });
+    process.on('unhandledRejection', (err) => {
+        console.error('[serve] unhandledRejection:', err);
+        shutdown('unhandledRejection', 1);
+    });
 });
 //# sourceMappingURL=serve.js.map

package/dist/cli/commands/serve.js.map

@@ -1 +1 @@
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package/dist/cli/commands/sync.d.ts

@@ -3,7 +3,7 @@
  *
  * Pull and push changes across the workspace:
  *   - the .studiograph config repo (if it has a git remote)
- *   - each entity collection that is a git repo with a remote
+ *   - each entity folder that is a git repo with a remote
  *
  * Works with both GitHub remotes and the embedded git server.
  */