studiograph 1.1.3 → 1.2.0-beta.2

package/dist/cli/commands/orphans.js

@@ -0,0 +1,125 @@
+/**
+ * studiograph orphans
+ *
+ * Finds entities with zero inbound wikilink references ("orphans")
+ * and optionally tombstones or deletes them.
+ */
+import { Command } from 'commander';
+import { Workspace } from '../../core/workspace.js';
+import { WorkspaceManager } from '../../core/workspace-manager.js';
+import { intro, outro, spinner, confirm } from '@clack/prompts';
+import { findOrphans } from '../../services/orphan-service.js';
+import { SyncStateManager } from '../../services/sync/sync-state.js';
+export const orphansCommand = new Command('orphans')
+    .description('Find entities with zero inbound references')
+    .option('--entity-types <types>', 'Comma-separated entity types to check (e.g. person,client)')
+    .option('--min-age <days>', 'Only flag entities older than N days', parseInt)
+    .option('--repos <repos>', 'Comma-separated repo names to scan')
+    .option('--tombstone', 'Add orphans to sync-state tombstones so future syncs skip them')
+    .option('--delete', 'Delete orphan entity files and tombstone them')
+    .option('--dry-run', 'Preview changes without modifying anything')
+    .action(async (options) => {
+    intro('Studiograph Orphans');
+    const s = spinner();
+    s.start('Loading workspace');
+    try {
+        const workspace = new Workspace();
+        if (!workspace.isWorkspace()) {
+            console.error('❌ Not a Studiograph workspace. Run `studiograph init` first.');
+            process.exit(1);
+        }
+        const config = await workspace.loadConfig();
+        const gitUser = { id: 'system', name: 'system', email: 'system@local' };
+        const cliUser = { id: 'system', name: 'system', email: 'system@local', role: 'admin' };
+        const manager = new WorkspaceManager(process.cwd(), config, gitUser, cliUser);
+        s.message('Scanning for orphans');
+        const filters = {
+            entityTypes: options.entityTypes?.split(',').map((t) => t.trim()),
+            minAgeDays: options.minAge,
+            repos: options.repos?.split(',').map((r) => r.trim()),
+        };
+        const result = findOrphans(manager, filters);
+        s.stop('Scan complete');
+        if (result.totalOrphans === 0) {
+            outro(`✅ No orphans found (scanned ${result.totalScanned} entities)`);
+            return;
+        }
+        // Group by entity type
+        const grouped = new Map();
+        for (const orphan of result.orphans) {
+            const key = orphan.entityType;
+            if (!grouped.has(key))
+                grouped.set(key, []);
+            grouped.get(key).push(orphan);
+        }
+        console.log('');
+        console.log(`Found ${result.totalOrphans} orphans (of ${result.totalScanned} scanned):\n`);
+        for (const [entityType, typeOrphans] of grouped.entries()) {
+            console.log(`${entityType.toUpperCase()} (${typeOrphans.length})`);
+            const examples = typeOrphans.slice(0, 10);
+            for (const orphan of examples) {
+                const name = orphan.name || orphan.entityId;
+                const age = orphan.createdAt
+                    ? `created ${orphan.createdAt}`
+                    : '';
+                console.log(`  - ${orphan.repo}/${orphan.entityType}/${orphan.entityId}${age ? `  (${age})` : ''}`);
+            }
+            if (typeOrphans.length > 10) {
+                console.log(`  ... and ${typeOrphans.length - 10} more`);
+            }
+            console.log('');
+        }
+        // Tombstone action
+        if (options.tombstone || options.delete) {
+            const action = options.delete ? 'delete and tombstone' : 'tombstone';
+            if (options.dryRun) {
+                console.log(`[dry-run] Would ${action} ${result.totalOrphans} orphan(s)`);
+                outro('Dry run complete');
+                return;
+            }
+            const shouldProceed = await confirm({
+                message: `${action === 'delete and tombstone' ? 'Delete' : 'Tombstone'} ${result.totalOrphans} orphan(s)?`,
+                initialValue: false,
+            });
+            if (!shouldProceed || typeof shouldProceed === 'symbol') {
+                outro('Cancelled');
+                return;
+            }
+            const actionSpinner = spinner();
+            actionSpinner.start(`Processing ${result.totalOrphans} orphans...`);
+            const syncState = new SyncStateManager(process.cwd());
+            let deleted = 0;
+            let tombstoned = 0;
+            for (const orphan of result.orphans) {
+                // Delete entity files if --delete
+                if (options.delete) {
+                    try {
+                        const graph = manager.getGraph(orphan.repo);
+                        await graph.delete(orphan.entityType, orphan.entityId);
+                        deleted++;
+                    }
+                    catch {
+                        // Entity might already be gone
+                    }
+                }
+                // Add to tombstones
+                syncState.addTombstone(orphan.entityId);
+                tombstoned++;
+            }
+            actionSpinner.stop('Done');
+            if (options.delete) {
+                console.log(`\nDeleted ${deleted} entities, tombstoned ${tombstoned}`);
+            }
+            else {
+                console.log(`\nTombstoned ${tombstoned} entities`);
+            }
+        }
+        outro('Orphan scan complete');
+    }
+    catch (error) {
+        s.stop('Error');
+        console.error('Failed to scan for orphans:', error instanceof Error ? error.message : error);
+        process.exit(1);
+    }
+});
+//# sourceMappingURL=orphans.js.map

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

@@ -0,0 +1 @@
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package/dist/cli/commands/provision.js

@@ -8,7 +8,7 @@ import { Command } from 'commander';
 import { intro, outro, spinner, log, confirm } from '@clack/prompts';
 import { execSync } from 'child_process';
 import { Workspace } from '../../core/workspace.js';
-import { loadToken, runDeviceFlow, storeToken, getGitHubUser, getAuthenticatedOctokit } from '../../auth/github.js';
+import { loadToken, promptForPAT, storeToken, getGitHubUser, getAuthenticatedOctokit } from '../../auth/github.js';
 import { provisionWorkspace } from '../../services/github-provisioner.js';
 import { runPreflight } from '../../utils/preflight.js';
 export const provisionCommand = new Command('provision')
@@ -56,7 +56,7 @@ export const provisionCommand = new Command('provision')
             log.info(`Using GitHub org from config: ${githubOrg}`);
         }
         if (!githubOrg) {
-            outro('❌ GitHub org required. Use --org <github-org>');
+            outro('❌ GitHub org required. Use: studiograph provision --org <github-org>');
             process.exit(1);
             return;
         }
@@ -64,7 +64,7 @@ export const provisionCommand = new Command('provision')
         let stored = loadToken();
         if (!stored) {
             log.info('No GitHub token found. Starting authentication...');
-            const token = await runDeviceFlow();
+            const token = await promptForPAT();
             const user = await getGitHubUser(token);
             storeToken(token, user);
             stored = { token, user };
@@ -74,7 +74,7 @@ export const provisionCommand = new Command('provision')
         // Provision!
         const provisionSpinner = spinner();
         provisionSpinner.start('Creating GitHub repos...');
-        const updatedConfig = await provisionWorkspace({
+        const result = await provisionWorkspace({
             octokit,
             org: githubOrg,
             workspacePath: workspace.getWorkspacePath(),
@@ -82,8 +82,8 @@ export const provisionCommand = new Command('provision')
             onProgress: (msg) => provisionSpinner.message(msg),
         });
         // Write back updated config with github_urls + org
-        updatedConfig.github = { org: githubOrg };
-        workspace.writeConfig(updatedConfig);
+        result.config.github = { org: githubOrg };
+        workspace.writeConfig(result.config);
         // Push updated workspace.json back to config repo
         provisionSpinner.message('Updating config repo with GitHub URLs...');
         const configPath = workspace.getWorkspacePath() + '/.studiograph';
@@ -99,13 +99,17 @@ export const provisionCommand = new Command('provision')
         // Show join URL
         const configRepoName = `${config.team_name.toLowerCase().replace(/[^a-z0-9]+/g, '-')}-config`;
         const configRepoUrl = `https://github.com/${githubOrg}/${configRepoName}.git`;
+        if (result.skipped.length > 0) {
+            log.warn(`Skipped ${result.skipped.length} repo(s) with no commits: ${result.skipped.join(', ')}`);
+            log.info('Commit content to these repos and re-run provision to push them.');
+        }
         log.success('All repos pushed to GitHub!');
         log.info('\nTo join this workspace from another machine:');
         log.info(`  studiograph join ${configRepoUrl}`);
         outro('✨ Workspace provisioned to GitHub!');
     }
     catch (error) {
-        outro(`❌ Error: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        outro(`Error: ${error instanceof Error ? error.message : 'Unknown error'}`);
         process.exit(1);
     }
 });

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

@@ -1 +1 @@
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package/dist/cli/commands/r2.js

@@ -8,7 +8,7 @@
  *                                     markdown files to R2, rewriting URLs in place
  */
 import { Command } from 'commander';
-import { intro, outro, text, spinner, log } from '@clack/prompts';
+import { intro, outro, text, confirm, spinner, log } from '@clack/prompts';
 import { readdirSync, statSync, readFileSync, writeFileSync, existsSync } from 'fs';
 import { join, relative, resolve, extname, dirname } from 'path';
 import { spawnSync } from 'child_process';
@@ -151,7 +151,13 @@ r2Command
         '  3. Copy the Access Key ID and Secret Access Key\n\n' +
         'Note: Admin access lets Studiograph create your bucket automatically.\n' +
         'You can replace this with a bucket-scoped token later for tighter security.');
-    openBrowser('https://dash.cloudflare.com/?to=/:account/r2/overview');
+    const openR2 = await confirm({ message: 'Open Cloudflare R2 dashboard in browser?' });
+    if (openR2) {
+        openBrowser('https://dash.cloudflare.com/?to=/:account/r2/overview');
+    }
+    else {
+        log.info('Open https://dash.cloudflare.com → R2 Object Storage to get your credentials');
+    }
     const accountId = await text({
         message: 'Account ID',
         placeholder: '32-character hex string',

package/dist/cli/commands/r2.js.map

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

@@ -0,0 +1,12 @@
+/**
+ * studiograph reset
+ *
+ * Reset a workspace by removing all entity data while preserving configuration.
+ * Keeps: .studiograph/ (config, team, migrations, sources, sync state)
+ * Removes: all repo directories (the entity markdown files)
+ *
+ * Useful for re-running sync pipelines from scratch or starting over
+ * without reconfiguring the workspace.
+ */
+import { Command } from 'commander';
+export declare const resetCommand: Command;

package/dist/cli/commands/reset.js

@@ -0,0 +1,137 @@
+/**
+ * studiograph reset
+ *
+ * Reset a workspace by removing all entity data while preserving configuration.
+ * Keeps: .studiograph/ (config, team, migrations, sources, sync state)
+ * Removes: all repo directories (the entity markdown files)
+ *
+ * Useful for re-running sync pipelines from scratch or starting over
+ * without reconfiguring the workspace.
+ */
+import { Command } from 'commander';
+import { existsSync, rmSync, readdirSync, statSync, readFileSync, writeFileSync } from 'fs';
+import { join, relative } from 'path';
+import { confirm, intro, isCancel, cancel } from '@clack/prompts';
+import { Workspace } from '../../core/workspace.js';
+export const resetCommand = new Command('reset')
+    .description('Reset workspace by removing all entity data (keeps config)')
+    .option('--yes', 'Skip confirmation prompt')
+    .option('--keep-sync-state', 'Preserve .studiograph/sync-state.json')
+    .action(async (opts) => {
+    const workspacePath = process.cwd();
+    const workspace = new Workspace(workspacePath);
+    if (!workspace.isWorkspace()) {
+        console.error('Not in a Studiograph workspace. Nothing to reset.');
+        process.exit(1);
+    }
+    const config = await workspace.loadConfig();
+    const repos = config.repos ?? [];
+    if (repos.length === 0) {
+        console.log('No repos registered in workspace config. Nothing to reset.');
+        return;
+    }
+    // Collect directories that will be removed
+    const toRemove = [];
+    for (const repo of repos) {
+        const repoPath = join(workspacePath, repo.path);
+        if (!existsSync(repoPath))
+            continue;
+        const entityCount = countEntities(repoPath);
+        toRemove.push({ name: repo.name, path: repoPath, entityCount });
+    }
+    if (toRemove.length === 0) {
+        console.log('All repo directories already removed. Nothing to reset.');
+        return;
+    }
+    // Show what will be removed
+    if (!opts.yes) {
+        intro('Workspace Reset');
+        console.log('This will remove all entity data:\n');
+        let totalEntities = 0;
+        for (const item of toRemove) {
+            const rel = relative(workspacePath, item.path);
+            console.log(`  ${rel.padEnd(30)} ${item.entityCount} entities`);
+            totalEntities += item.entityCount;
+        }
+        console.log(`\n  Total: ${totalEntities} entities across ${toRemove.length} repos`);
+        console.log('\n  Preserved: .studiograph/ (config, team, migrations)');
+        const proceed = await confirm({
+            message: 'Are you sure you want to reset?',
+        });
+        if (isCancel(proceed) || !proceed) {
+            cancel('Reset cancelled.');
+            process.exit(0);
+        }
+    }
+    // Remove repo directories
+    for (const item of toRemove) {
+        rmSync(item.path, { recursive: true, force: true });
+        console.log(`  Removed ${item.name} (${item.entityCount} entities)`);
+    }
+    // Optionally clear sync state (preserving tombstones)
+    if (!opts.keepSyncState) {
+        const syncStatePath = join(workspacePath, '.studiograph', 'sync-state.json');
+        if (existsSync(syncStatePath)) {
+            let tombstones = [];
+            try {
+                const existing = JSON.parse(readFileSync(syncStatePath, 'utf-8'));
+                tombstones = existing.tombstones ?? [];
+            }
+            catch { /* ignore parse errors */ }
+            writeFileSync(syncStatePath, JSON.stringify({ sources: {}, tombstones }, null, 2) + '\n', 'utf-8');
+            if (tombstones.length > 0) {
+                console.log(`  Cleared sync state (preserved ${tombstones.length} tombstones)`);
+            }
+            else {
+                console.log('  Cleared sync state');
+            }
+        }
+        const populateCachePath = join(workspacePath, '.studiograph', 'populate-cache');
+        if (existsSync(populateCachePath)) {
+            rmSync(populateCachePath, { recursive: true, force: true });
+            console.log('  Cleared populate cache');
+        }
+        const stagingPath = join(workspacePath, '.studiograph', 'staging');
+        if (existsSync(stagingPath)) {
+            rmSync(stagingPath, { recursive: true, force: true });
+            console.log('  Cleared staging');
+        }
+    }
+    // Remove private graph if it exists
+    const privatePath = join(workspacePath, 'private');
+    if (existsSync(privatePath)) {
+        rmSync(privatePath, { recursive: true, force: true });
+        console.log('  Removed private graph');
+    }
+    console.log('\nWorkspace reset complete. Config preserved at .studiograph/');
+    console.log('Re-run sync or create entities to repopulate.');
+});
+/**
+ * Count .md files recursively in a directory.
+ */
+function countEntities(dir) {
+    let count = 0;
+    try {
+        const entries = readdirSync(dir);
+        for (const entry of entries) {
+            const full = join(dir, entry);
+            try {
+                const stat = statSync(full);
+                if (stat.isDirectory()) {
+                    count += countEntities(full);
+                }
+                else if (entry.endsWith('.md')) {
+                    count++;
+                }
+            }
+            catch {
+                // skip inaccessible entries
+            }
+        }
+    }
+    catch {
+        // skip inaccessible directories
+    }
+    return count;
+}
+//# sourceMappingURL=reset.js.map

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

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package/dist/cli/commands/review.d.ts

@@ -0,0 +1,19 @@
+/**
+ * studiograph review
+ *
+ * Review uncommitted or recently committed entity changes across workspace repos.
+ * Works after sync commit, enrich run, manual edits, or any other modification.
+ *
+ *   studiograph review                — interactive review (auto-detects uncommitted vs committed)
+ *   studiograph review --type task    — show colored diff for an entity type
+ *   studiograph review --file <path>  — show colored diff for a specific file
+ *   studiograph review --committed    — review last commit instead of uncommitted changes
+ */
+import { Command } from 'commander';
+export interface ReviewOptions {
+    type?: string;
+    file?: string;
+    committed?: boolean;
+}
+export declare function runReview(opts: ReviewOptions): Promise<void>;
+export declare const reviewCommand: Command;

package/dist/cli/commands/review.js

@@ -0,0 +1,128 @@
+/**
+ * studiograph review
+ *
+ * Review uncommitted or recently committed entity changes across workspace repos.
+ * Works after sync commit, enrich run, manual edits, or any other modification.
+ *
+ *   studiograph review                — interactive review (auto-detects uncommitted vs committed)
+ *   studiograph review --type task    — show colored diff for an entity type
+ *   studiograph review --file <path>  — show colored diff for a specific file
+ *   studiograph review --committed    — review last commit instead of uncommitted changes
+ */
+import { Command } from 'commander';
+import { spawnSync } from 'child_process';
+import { existsSync } from 'fs';
+import { join } from 'path';
+import { Workspace } from '../../core/workspace.js';
+import { isGitRepo, gitHasUncommittedChanges } from '../../utils/git.js';
+import { loadWorkspaceConfig } from '../../utils/workspace-config.js';
+import { header, dimText, colorizeDiff } from '../colors.js';
+import { detectDiffMode, runInteractiveReview } from '../sync-review-interactive.js';
+export async function runReview(opts) {
+    const workspace = new Workspace(process.cwd());
+    if (!workspace.isWorkspace()) {
+        console.error('Not in a Studiograph workspace.');
+        process.exit(1);
+    }
+    const config = loadWorkspaceConfig(process.cwd());
+    const repos = (config?.repos ?? []).map((r) => ({
+        name: r.name,
+        path: r.path,
+    }));
+    const gitRepos = repos.filter((r) => {
+        const p = join(process.cwd(), r.path);
+        return existsSync(p) && isGitRepo(p);
+    });
+    if (gitRepos.length === 0) {
+        console.log('No git repositories found in workspace.');
+        return;
+    }
+    // Determine diff mode
+    const useCommitted = opts.committed ?? (detectDiffMode(process.cwd(), gitRepos) === 'committed');
+    const diffArgs = useCommitted
+        ? ['diff', 'HEAD~1..HEAD']
+        : ['diff'];
+    // ── Non-interactive: --file ──────────────────────────────────────────────
+    if (opts.file) {
+        for (const repo of gitRepos) {
+            const repoPath = join(process.cwd(), repo.path);
+            const result = spawnSync('git', [...diffArgs, '--', opts.file], { cwd: repoPath, encoding: 'utf-8' });
+            if (result.status === 0 && result.stdout.trim()) {
+                console.log(colorizeDiff(result.stdout));
+                return;
+            }
+        }
+        console.log(`No changes found for ${opts.file}`);
+        return;
+    }
+    // ── Non-interactive: --type ──────────────────────────────────────────────
+    if (opts.type) {
+        let found = false;
+        for (const repo of gitRepos) {
+            const repoPath = join(process.cwd(), repo.path);
+            const result = spawnSync('git', [...diffArgs, '--', `${opts.type}/`], { cwd: repoPath, encoding: 'utf-8' });
+            if (result.status === 0 && result.stdout.trim()) {
+                console.log(colorizeDiff(result.stdout));
+                found = true;
+            }
+        }
+        if (!found) {
+            console.log(`No changes found for type "${opts.type}"`);
+        }
+        return;
+    }
+    // ── Interactive mode ─────────────────────────────────────────────────────
+    if (process.stdout.isTTY) {
+        await runInteractiveReview({
+            workspacePath: process.cwd(),
+            repos: gitRepos,
+            committed: useCommitted,
+        });
+        if (!useCommitted)
+            printNextSteps(process.cwd(), gitRepos);
+        return;
+    }
+    // ── Non-interactive fallback (piped output) ──────────────────────────────
+    let totalChanged = 0;
+    console.log(`${header('Entity changes')}:\n`);
+    for (const repo of gitRepos) {
+        const repoPath = join(process.cwd(), repo.path);
+        const result = spawnSync('git', [...diffArgs, '--stat'], { cwd: repoPath, encoding: 'utf-8' });
+        if (result.status === 0 && result.stdout.trim()) {
+            console.log(`  ${header(repo.name + '/')}`);
+            for (const line of result.stdout.trim().split('\n')) {
+                console.log(`    ${line}`);
+                totalChanged++;
+            }
+            console.log();
+        }
+    }
+    if (totalChanged === 0) {
+        console.log('No changes in any repo.');
+    }
+    else {
+        console.log(`Review with: ${header('studiograph review --type <type>')}`);
+        if (!useCommitted)
+            printNextSteps(process.cwd(), gitRepos);
+    }
+}
+/** Print next-steps guidance when uncommitted changes remain. */
+function printNextSteps(workspacePath, repos) {
+    const hasChanges = repos.some((r) => {
+        const p = join(workspacePath, r.path);
+        return existsSync(p) && isGitRepo(p) && gitHasUncommittedChanges(p);
+    });
+    if (!hasChanges)
+        return;
+    console.log(`\nNext: ${header('studiograph commit')}       ${dimText('(git commit changes)')}`);
+    console.log(`Or:   ${dimText('git checkout -- .')}         ${dimText('(discard all changes)')}`);
+}
+export const reviewCommand = new Command('review')
+    .description('Review entity changes across workspace repos')
+    .option('--type <entity_type>', 'Show colored diff for an entity type')
+    .option('--file <path>', 'Show colored diff for a specific file')
+    .option('--committed', 'Review last commit instead of uncommitted changes')
+    .action(async (opts) => {
+    await runReview(opts);
+});
+//# sourceMappingURL=review.js.map

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

@@ -0,0 +1 @@
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