studiograph 1.1.2 → 1.2.0-beta.1

package/dist/services/orphan-service.js

@@ -0,0 +1,100 @@
+/**
+ * Orphan Entity Detection Service
+ *
+ * Finds entities with zero inbound wikilink references across the entire graph.
+ * These are "orphans" — they exist but nothing points to them.
+ *
+ * Supports filtering by entity type, minimum age, and actions like
+ * tombstoning (sync-state) or deletion.
+ */
+import { MarkdownService, slugifyWikilink } from './markdown.js';
+/**
+ * Build a set of all entity IDs that are referenced by at least one wikilink
+ * anywhere in the graph. An entity NOT in this set is an orphan.
+ */
+function buildReferencedSet(manager, markdown) {
+    const referenced = new Set();
+    const allRepos = manager.getAllRepoConfigs();
+    for (const repoConfig of allRepos) {
+        let graph;
+        try {
+            graph = manager.getGraph(repoConfig.name);
+        }
+        catch {
+            continue;
+        }
+        const entities = graph.list();
+        for (const entity of entities) {
+            // Collect all wikilinks from this entity's content + frontmatter
+            for (const link of entity.document.wikilinks) {
+                // Normalize: strip repo prefix if present, then slugify
+                const cleanLink = link.split('/').pop() || link;
+                referenced.add(cleanLink);
+                referenced.add(slugifyWikilink(cleanLink));
+            }
+        }
+    }
+    return referenced;
+}
+/**
+ * Find all orphan entities — entities with zero inbound wikilink references.
+ */
+export function findOrphans(manager, filters) {
+    const markdown = new MarkdownService();
+    const referenced = buildReferencedSet(manager, markdown);
+    const allRepos = manager.getAllRepoConfigs();
+    const repos = filters?.repos
+        ? allRepos.filter(r => filters.repos.includes(r.name))
+        : allRepos;
+    const entityTypeFilter = filters?.entityTypes
+        ? new Set(filters.entityTypes)
+        : null;
+    const now = Date.now();
+    const minAgeMs = (filters?.minAgeDays ?? 0) * 86_400_000;
+    const orphans = [];
+    let totalScanned = 0;
+    for (const repoConfig of repos) {
+        let graph;
+        try {
+            graph = manager.getGraph(repoConfig.name);
+        }
+        catch {
+            continue;
+        }
+        const entities = graph.list();
+        for (const entity of entities) {
+            const entityType = entity.data.entity_type;
+            // Filter by entity type
+            if (entityTypeFilter && !entityTypeFilter.has(entityType))
+                continue;
+            totalScanned++;
+            // Check if this entity is referenced anywhere
+            const id = entity.id;
+            if (referenced.has(id) || referenced.has(slugifyWikilink(id))) {
+                continue;
+            }
+            // Check minimum age
+            if (minAgeMs > 0) {
+                const createdStr = entity.data.created_at;
+                if (createdStr) {
+                    const createdMs = new Date(createdStr).getTime();
+                    if (now - createdMs < minAgeMs)
+                        continue;
+                }
+            }
+            orphans.push({
+                repo: repoConfig.name,
+                entityType,
+                entityId: id,
+                createdAt: entity.data.created_at,
+                name: entity.data.name,
+            });
+        }
+    }
+    return {
+        orphans,
+        totalScanned,
+        totalOrphans: orphans.length,
+    };
+}
+//# sourceMappingURL=orphan-service.js.map

package/dist/services/orphan-service.js.map

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package/dist/services/sync/commit.d.ts

@@ -0,0 +1,58 @@
+/**
+ * Commit staging files to the graph.
+ *
+ * Reads staging files, filters out _action: skip, strips _* metadata,
+ * and uses MarkdownService to write to repos. Persists provenance to
+ * SyncState before stripping. Records explicit skips as tombstones.
+ *
+ * For updates, performs field-level merge: sync only overwrites fields
+ * it owns (tracked via field_origins). User-added fields are preserved.
+ *
+ * Exports:
+ *   applyStaging()  — write staging → entity files (no git)
+ *   commitRepos()   — git commit across workspace repos
+ *   commitStaging() — backwards-compatible wrapper (apply + git)
+ */
+export interface CommitResult {
+    created: number;
+    updated: number;
+    skipped: number;
+}
+export interface ApplyResult extends CommitResult {
+    /** Per-repo stats for building git commit messages. */
+    perRepo: Map<string, {
+        created: number;
+        updated: number;
+        sources: Set<string>;
+    }>;
+}
+export interface CommitOptions {
+    force?: boolean;
+    noGit?: boolean;
+}
+export interface CommitReposOptions {
+    /** Prefix for the commit message (e.g. "sync", "enrich"). Default: "sync" */
+    messagePrefix?: string;
+    /** Per-repo stats from applyStaging() — used to build detailed commit messages. */
+    perRepo?: Map<string, {
+        created: number;
+        updated: number;
+        sources: Set<string>;
+    }>;
+}
+/**
+ * Write staging files to entity files on disk. Does NOT touch git.
+ * Handles: dirty tree check, staging read, field-level merge, entity file
+ * writes, staging clear, and sync state update.
+ */
+export declare function applyStaging(workspacePath: string, onProgress?: (msg: string) => void, options?: Pick<CommitOptions, 'force'>): Promise<ApplyResult>;
+/**
+ * Git commit uncommitted changes across workspace repos.
+ * Works after applyStaging(), enrich, or any manual edits.
+ */
+export declare function commitRepos(workspacePath: string, onProgress?: (msg: string) => void, options?: CommitReposOptions): Promise<void>;
+/**
+ * Write staging files to the graph and optionally git-commit.
+ * Backwards-compatible wrapper around applyStaging() + commitRepos().
+ */
+export declare function commitStaging(workspacePath: string, onProgress?: (msg: string) => void, options?: CommitOptions): Promise<CommitResult>;

package/dist/services/sync/commit.js

@@ -0,0 +1,350 @@
+/**
+ * Commit staging files to the graph.
+ *
+ * Reads staging files, filters out _action: skip, strips _* metadata,
+ * and uses MarkdownService to write to repos. Persists provenance to
+ * SyncState before stripping. Records explicit skips as tombstones.
+ *
+ * For updates, performs field-level merge: sync only overwrites fields
+ * it owns (tracked via field_origins). User-added fields are preserved.
+ *
+ * Exports:
+ *   applyStaging()  — write staging → entity files (no git)
+ *   commitRepos()   — git commit across workspace repos
+ *   commitStaging() — backwards-compatible wrapper (apply + git)
+ */
+import { existsSync, mkdirSync, writeFileSync } from 'fs';
+import { join } from 'path';
+import { spawnSync } from 'child_process';
+import { MarkdownService } from '../../services/markdown.js';
+import { StagingManager } from './staging.js';
+import { SyncStateManager } from './sync-state.js';
+import { gitHasUncommittedChanges, isGitRepo } from '../../utils/git.js';
+import { loadWorkspaceConfig } from '../../utils/workspace-config.js';
+import { Workspace } from '../../core/workspace.js';
+import { RepoType } from '../../core/types.js';
+import { reindexWorkspace } from '../vector-service.js';
+/** Base entity fields that sync always controls. */
+const BASE_FIELDS = new Set([
+    'entity_type', 'entity_id', 'updated_at', 'updated_by',
+]);
+// ── applyStaging ──────────────────────────────────────────────────────────────
+/**
+ * Write staging files to entity files on disk. Does NOT touch git.
+ * Handles: dirty tree check, staging read, field-level merge, entity file
+ * writes, staging clear, and sync state update.
+ */
+export async function applyStaging(workspacePath, onProgress, options) {
+    const log = onProgress ?? (() => { });
+    const staging = new StagingManager(workspacePath);
+    const syncState = new SyncStateManager(workspacePath);
+    const markdown = new MarkdownService();
+    const files = staging.readStaging();
+    if (files.length === 0) {
+        log('No staging files to apply.');
+        return { created: 0, updated: 0, skipped: 0, perRepo: new Map() };
+    }
+    // Load workspace config for repo paths
+    const config = loadWorkspaceConfig(workspacePath);
+    let repos = config?.repos ?? [];
+    // ── Auto-register unknown repos ───────────────────────────────────────
+    if (config) {
+        const targetRepoNames = new Set(files.filter(f => f.frontmatter._action !== 'skip').map(f => f.repo));
+        for (const repoName of targetRepoNames) {
+            if (!repos.find((r) => r.name === repoName)) {
+                log(`  Auto-registering repo: ${repoName}`);
+                const workspace = new Workspace(workspacePath);
+                await workspace.registerRepo({ name: repoName, type: RepoType.PROJECT });
+                // Reload config to pick up new repo
+                const updatedConfig = loadWorkspaceConfig(workspacePath);
+                repos = updatedConfig?.repos ?? [];
+            }
+        }
+    }
+    // ── Dirty working tree check (per-repo) ─────────────────────────────────
+    if (!options?.force) {
+        const targetRepoPaths = new Set();
+        for (const file of files) {
+            if (file.frontmatter._action === 'skip')
+                continue;
+            const repo = repos.find((r) => r.name === file.repo);
+            const repoPath = repo ? join(workspacePath, repo.path) : join(workspacePath, file.repo);
+            targetRepoPaths.add(repoPath);
+        }
+        for (const repoPath of targetRepoPaths) {
+            if (existsSync(repoPath) && isGitRepo(repoPath) && gitHasUncommittedChanges(repoPath)) {
+                const msg = `Uncommitted changes in ${repoPath}. Commit or stash changes first, or use --force.`;
+                log(msg);
+                throw new Error(msg);
+            }
+        }
+    }
+    const result = { created: 0, updated: 0, skipped: 0, perRepo: new Map() };
+    for (const file of files) {
+        const action = file.frontmatter._action;
+        const fieldSources = (file.frontmatter._field_sources ?? {});
+        // Save provenance before stripping
+        const sources = file.frontmatter._sources;
+        if (sources && sources.length > 0) {
+            for (const sourceRef of sources) {
+                const sourceName = sourceRef.split(':')[0] ?? sourceRef.split('/')[0] ?? 'unknown';
+                syncState.setEntityMapping(sourceName, file.entity_id, sourceRef);
+            }
+        }
+        if (action === 'skip') {
+            // Track as tombstone if user explicitly changed from create to skip
+            syncState.addTombstone(file.entity_id);
+            result.skipped++;
+            log(`  Skipped: ${file.entity_type}/${file.entity_id}`);
+            continue;
+        }
+        // Strip staging metadata fields
+        const stagedFrontmatter = { ...file.frontmatter };
+        const coLocate = stagedFrontmatter._co_locate;
+        const writeMode = stagedFrontmatter._write_mode;
+        delete stagedFrontmatter._action;
+        delete stagedFrontmatter._confidence;
+        delete stagedFrontmatter._sources;
+        delete stagedFrontmatter._notes;
+        delete stagedFrontmatter._field_sources;
+        delete stagedFrontmatter._co_locate;
+        delete stagedFrontmatter._write_mode;
+        // Determine target path
+        const repo = repos.find((r) => r.name === file.repo);
+        const repoPath = repo ? join(workspacePath, repo.path) : join(workspacePath, file.repo);
+        // Git-init new repo directories immediately so they're protected from
+        // manual resets or git clean even if workspace_commit isn't called later.
+        if (!existsSync(repoPath)) {
+            mkdirSync(repoPath, { recursive: true });
+        }
+        if (!isGitRepo(repoPath)) {
+            spawnSync('git', ['init'], { cwd: repoPath, encoding: 'utf-8' });
+            const ignorePath = join(repoPath, '.gitignore');
+            if (!existsSync(ignorePath)) {
+                writeFileSync(ignorePath, '.DS_Store\n*.tmp\n*.log\n', 'utf-8');
+            }
+        }
+        let entityPath;
+        if (coLocate) {
+            // Co-located sub-content: {repo}/{parentId}/{subfolder}/{entityId}.md
+            const parentRef = stagedFrontmatter[coLocate.parent_field];
+            if (!parentRef) {
+                result.skipped++;
+                log(`  Skipped: ${file.entity_type}/${file.entity_id} (no ${coLocate.parent_field} assigned)`);
+                continue;
+            }
+            const parentId = parentRef.replace(/^\[\[/, '').replace(/\]\]$/, '');
+            const subDir = join(repoPath, parentId, coLocate.subfolder);
+            mkdirSync(subDir, { recursive: true });
+            entityPath = join(subDir, `${file.entity_id}.md`);
+        }
+        else if (writeMode === 'collection') {
+            // Collection mode: {repo}/{entityId}.md (loose file, no subfolder)
+            mkdirSync(repoPath, { recursive: true });
+            entityPath = join(repoPath, `${file.entity_id}.md`);
+        }
+        else {
+            // Standard entity: {repo}/{entityId}/main.md
+            const entityDir = join(repoPath, file.entity_id);
+            mkdirSync(entityDir, { recursive: true });
+            entityPath = join(entityDir, 'main.md');
+        }
+        const now = new Date().toISOString();
+        let finalFrontmatter;
+        if (action === 'update' && existsSync(entityPath)) {
+            // ── Field-level merge ─────────────────────────────────────────────
+            const existing = markdown.parseFile(entityPath);
+            finalFrontmatter = { ...existing.frontmatter };
+            // Overwrite source-owned fields and base fields
+            for (const [key, value] of Object.entries(stagedFrontmatter)) {
+                if (BASE_FIELDS.has(key) || fieldSources[key]) {
+                    finalFrontmatter[key] = value;
+                }
+                else if (finalFrontmatter[key] === undefined) {
+                    // New field from sync that wasn't on disk — add it
+                    finalFrontmatter[key] = value;
+                }
+                // else: field exists on disk and sync doesn't own it → preserve user value
+            }
+            // Preserve created_at/created_by from existing
+            if (existing.frontmatter.created_at)
+                finalFrontmatter.created_at = existing.frontmatter.created_at;
+            if (existing.frontmatter.created_by)
+                finalFrontmatter.created_by = existing.frontmatter.created_by;
+            // Always update timestamps
+            finalFrontmatter.updated_at = now;
+            finalFrontmatter.updated_by = 'sync';
+        }
+        else {
+            // ── Create (or update with no existing file) ──────────────────────
+            finalFrontmatter = stagedFrontmatter;
+            // Add base entity fields if missing
+            if (!finalFrontmatter.entity_type)
+                finalFrontmatter.entity_type = file.entity_type;
+            if (!finalFrontmatter.entity_id)
+                finalFrontmatter.entity_id = file.entity_id;
+            if (!finalFrontmatter.created_at)
+                finalFrontmatter.created_at = now;
+            if (!finalFrontmatter.updated_at)
+                finalFrontmatter.updated_at = now;
+            if (!finalFrontmatter.created_by)
+                finalFrontmatter.created_by = 'sync';
+            if (!finalFrontmatter.updated_by)
+                finalFrontmatter.updated_by = 'sync';
+        }
+        markdown.writeFile(entityPath, {
+            frontmatter: finalFrontmatter,
+            content: file.content,
+            wikilinks: [],
+        });
+        // Track per-repo stats for git commit messages
+        if (!result.perRepo.has(repoPath)) {
+            result.perRepo.set(repoPath, { created: 0, updated: 0, sources: new Set() });
+        }
+        const repoStats = result.perRepo.get(repoPath);
+        const sourceRefs = file.frontmatter._sources;
+        if (sourceRefs) {
+            for (const ref of sourceRefs) {
+                const name = ref.split('/')[0];
+                if (name)
+                    repoStats.sources.add(name);
+            }
+        }
+        // Persist field origins to sync state
+        if (Object.keys(fieldSources).length > 0) {
+            // Group field_sources by source name
+            const bySource = new Map();
+            for (const [field, source] of Object.entries(fieldSources)) {
+                if (!bySource.has(source))
+                    bySource.set(source, {});
+                bySource.get(source)[field] = source;
+            }
+            for (const [sourceName, fields] of bySource) {
+                syncState.setFieldOrigins(sourceName, file.entity_id, fields);
+            }
+        }
+        if (action === 'update') {
+            result.updated++;
+            repoStats.updated++;
+            log(`  Updated: ${file.entity_type}/${file.entity_id}`);
+        }
+        else {
+            result.created++;
+            repoStats.created++;
+            log(`  Created: ${file.entity_type}/${file.entity_id}`);
+        }
+    }
+    // Clear staging after successful apply
+    staging.clear();
+    log(`\nApply complete: ${result.created} created, ${result.updated} updated, ${result.skipped} skipped`);
+    return result;
+}
+// ── commitRepos ───────────────────────────────────────────────────────────────
+/**
+ * Git commit uncommitted changes across workspace repos.
+ * Works after applyStaging(), enrich, or any manual edits.
+ */
+export async function commitRepos(workspacePath, onProgress, options) {
+    const log = onProgress ?? (() => { });
+    const prefix = options?.messagePrefix ?? 'sync';
+    const perRepo = options?.perRepo;
+    // ── Reconcile workspace.json with filesystem ────────────────────────
+    const workspace = new Workspace(workspacePath);
+    if (workspace.isWorkspace()) {
+        const { added, removed } = await workspace.reconcileRepos();
+        for (const name of added)
+            log(`  Registered repo: ${name}`);
+        for (const name of removed)
+            log(`  Removed stale repo: ${name}`);
+        // Commit .studiograph/ if workspace.json changed
+        if (added.length > 0 || removed.length > 0) {
+            const sgDir = join(workspacePath, '.studiograph');
+            if (isGitRepo(workspacePath) && gitHasUncommittedChanges(workspacePath)) {
+                spawnSync('git', ['add', sgDir], { cwd: workspacePath, encoding: 'utf-8' });
+                const parts = [];
+                if (added.length > 0)
+                    parts.push(`add ${added.join(', ')}`);
+                if (removed.length > 0)
+                    parts.push(`remove ${removed.join(', ')}`);
+                const msg = `workspace: reconcile repos (${parts.join('; ')})`;
+                spawnSync('git', ['commit', '-m', msg], { cwd: workspacePath, encoding: 'utf-8' });
+                log(`  Committed workspace.json update`);
+            }
+        }
+    }
+    const config = loadWorkspaceConfig(workspacePath);
+    const repos = config?.repos ?? [];
+    for (const repo of repos) {
+        const repoPath = join(workspacePath, repo.path);
+        if (!existsSync(repoPath))
+            continue;
+        // Initialize git repo if it doesn't exist yet
+        if (!isGitRepo(repoPath)) {
+            const init = spawnSync('git', ['init'], { cwd: repoPath, encoding: 'utf-8' });
+            if (init.status !== 0) {
+                log(`  Warning: git init failed in ${repoPath}: ${init.stderr?.trim()}`);
+                continue;
+            }
+            const ignorePath = join(repoPath, '.gitignore');
+            if (!existsSync(ignorePath)) {
+                writeFileSync(ignorePath, '.DS_Store\n*.tmp\n*.log\n', 'utf-8');
+            }
+            log(`  Git init: ${repo.name}`);
+        }
+        if (!gitHasUncommittedChanges(repoPath))
+            continue;
+        // Build commit message
+        let commitMsg;
+        const stats = perRepo?.get(repoPath);
+        if (stats) {
+            const parts = [];
+            if (stats.created > 0)
+                parts.push(`${stats.created} created`);
+            if (stats.updated > 0)
+                parts.push(`${stats.updated} updated`);
+            const from = stats.sources.size > 0 ? ` from ${[...stats.sources].join(', ')}` : '';
+            commitMsg = `${prefix}: ${parts.join(', ')}${from}`;
+        }
+        else {
+            // Generic message — count changed files from git status
+            const status = spawnSync('git', ['status', '--porcelain'], { cwd: repoPath, encoding: 'utf-8' });
+            const changedFiles = (status.stdout?.trim().split('\n').filter(Boolean) ?? []).length;
+            commitMsg = `${prefix}: ${changedFiles} file${changedFiles === 1 ? '' : 's'} changed`;
+        }
+        // Stage all changes within this repo directory (relies on .gitignore for exclusions)
+        const add = spawnSync('git', ['add', '.'], { cwd: repoPath, encoding: 'utf-8' });
+        if (add.status !== 0) {
+            log(`  Warning: git add failed in ${repoPath}: ${add.stderr?.trim()}`);
+            continue;
+        }
+        const commit = spawnSync('git', ['commit', '-m', commitMsg], { cwd: repoPath, encoding: 'utf-8' });
+        if (commit.status === 0) {
+            log(`  Git commit: ${repo.name}`);
+        }
+        else {
+            log(`  Warning: git commit failed in ${repoPath}: ${commit.stderr?.trim()}`);
+        }
+    }
+    // Reindex search after commit (non-fatal)
+    try {
+        const indexed = await reindexWorkspace(workspacePath, repos, log);
+        if (indexed > 0)
+            log(`  Search index updated (${indexed} entities)`);
+    }
+    catch {
+        // Non-fatal — search may be stale until next manual reindex
+    }
+}
+// ── commitStaging (backwards-compatible wrapper) ──────────────────────────────
+/**
+ * Write staging files to the graph and optionally git-commit.
+ * Backwards-compatible wrapper around applyStaging() + commitRepos().
+ */
+export async function commitStaging(workspacePath, onProgress, options) {
+    const applyResult = await applyStaging(workspacePath, onProgress, { force: options?.force });
+    if (!options?.noGit) {
+        await commitRepos(workspacePath, onProgress, { perRepo: applyResult.perRepo });
+    }
+    return { created: applyResult.created, updated: applyResult.updated, skipped: applyResult.skipped };
+}
+//# sourceMappingURL=commit.js.map

package/dist/services/sync/commit.js.map

@@ -0,0 +1 @@
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package/dist/services/sync/context-index.d.ts

@@ -0,0 +1,69 @@
+/**
+ * ContextIndex
+ *
+ * Cross-source context index for enrichment. Scans all repos for entity
+ * references using schema relationship fields and wikilinks.
+ *
+ * Ranks references by recency, enforces a max_tokens budget, and truncates
+ * excess context before the LLM call.
+ */
+import type { SchemaRegistry } from '../../core/schema-registry.js';
+export interface ContextReference {
+    entity_id: string;
+    entity_type: string;
+    field: string;
+    repo: string;
+    /** ISO date for recency ranking */
+    date?: string;
+    /** Short summary snippet */
+    snippet: string;
+}
+export interface EnrichableEntity {
+    entity_id: string;
+    entity_type: string;
+    repo: string;
+    path: string;
+    frontmatter: Record<string, any>;
+    completeness: number;
+    refCount: number;
+}
+export declare class ContextIndex {
+    private workspacePath;
+    private schemaRegistry;
+    private markdownService;
+    private references;
+    private built;
+    constructor(workspacePath: string, schemaRegistry: SchemaRegistry);
+    /**
+     * Scan all repos for entity references.
+     */
+    build(): void;
+    /**
+     * Get all context references for one entity.
+     */
+    getReferences(entityId: string): ContextReference[];
+    /**
+     * Calculate field completeness (0–1) for an entity.
+     */
+    getCompleteness(entityType: string, frontmatter: Record<string, any>): number;
+    /**
+     * Filter to entities worth enriching (low completeness + high context).
+     */
+    getEnrichable(minRefs?: number, maxCompleteness?: number): EnrichableEntity[];
+    /**
+     * Assemble LLM context bundle for one entity.
+     * Ranks references by recency, enforces max_tokens budget.
+     */
+    assembleContextBundle(entityId: string, entityName: string, maxTokens?: number): string;
+    private scanRepo;
+    private addReference;
+    /**
+     * Get relationship fields for an entity type by inspecting schema descriptions.
+     */
+    private getRelationshipFields;
+    private getDescription;
+    private extractEntityId;
+    private makeSnippet;
+    private findRepoDirs;
+    private listSubDirs;
+}