studiograph 1.1.3 → 1.2.0-beta.10

package/dist/services/sync/unstructured-extractor.d.ts

@@ -0,0 +1,29 @@
+/**
+ * UnstructuredExtractor
+ *
+ * Extracts entities from file-based sources (e.g. Obsidian) where field
+ * mapping isn't possible. Uses LLM for extraction.
+ */
+import { SyncMCPClient } from './mcp-client.js';
+import type { SchemaRegistry } from '../../core/schema-registry.js';
+import type { GraphRAGClient } from './graphrag-client.js';
+import type { SourceConfig, EntityMapping, ExtractedRecord, SourceFile } from './types.js';
+export declare class UnstructuredExtractor {
+    private client;
+    private sourceConfig;
+    private schemaRegistry;
+    private graphrag?;
+    constructor(client: SyncMCPClient, sourceConfig: SourceConfig, schemaRegistry: SchemaRegistry, graphrag?: GraphRAGClient);
+    /**
+     * Discover files matching directory patterns.
+     */
+    discover(mapping: EntityMapping): Promise<SourceFile[]>;
+    /**
+     * Extract one file via LLM.
+     */
+    extractOne(file: SourceFile, mapping: EntityMapping, onProgress?: (msg: string) => void): Promise<ExtractedRecord | null>;
+    /**
+     * Extract all files for one mapping (with concurrency limit).
+     */
+    extract(mapping: EntityMapping, onProgress?: (msg: string) => void): Promise<ExtractedRecord[]>;
+}

package/dist/services/sync/unstructured-extractor.js

@@ -0,0 +1,197 @@
+/**
+ * UnstructuredExtractor
+ *
+ * Extracts entities from file-based sources (e.g. Obsidian) where field
+ * mapping isn't possible. Uses LLM for extraction.
+ */
+import { llmExtract } from './llm.js';
+import { slugify } from './structured-extractor.js';
+import { matchGlob } from './frontmatter-extractor.js';
+const CONCURRENCY_LIMIT = 3;
+export class UnstructuredExtractor {
+    client;
+    sourceConfig;
+    schemaRegistry;
+    graphrag;
+    constructor(client, sourceConfig, schemaRegistry, graphrag) {
+        this.client = client;
+        this.sourceConfig = sourceConfig;
+        this.schemaRegistry = schemaRegistry;
+        this.graphrag = graphrag;
+    }
+    /**
+     * Discover files matching directory patterns.
+     */
+    async discover(mapping) {
+        // Use explicit tool name from mapping, or fall back to heuristic matching
+        const tools = this.client.getTools();
+        const listTool = mapping.list_tool
+            ? tools.find(t => t.name === mapping.list_tool)
+            : tools.find(t => t.name.includes('list') && (t.name.includes('file') || t.name.includes('vault')));
+        if (!listTool) {
+            throw new Error(mapping.list_tool
+                ? `Configured list_tool "${mapping.list_tool}" not found on the MCP server`
+                : 'No file listing tool found on the MCP server');
+        }
+        const files = [];
+        const patterns = mapping.directory_patterns ?? [];
+        if (patterns.length === 0) {
+            // List all files
+            const raw = await this.client.callTool(listTool.name);
+            const items = parseFileList(raw);
+            for (const item of items) {
+                const path = typeof item === 'string' ? item : (item.path ?? item.filename ?? item.name);
+                if (path && path.endsWith('.md')) {
+                    if (mapping.file_pattern) {
+                        const basename = (path.split('/').pop() ?? path).replace(/\.md$/, '');
+                        if (!matchGlob(mapping.file_pattern, basename))
+                            continue;
+                    }
+                    if (mapping.name_match === 'folder') {
+                        const parts = path.split('/');
+                        const basename = (parts[parts.length - 1] ?? path).replace(/\.md$/, '');
+                        const parentFolder = parts.length >= 2 ? parts[parts.length - 2] : '';
+                        if (basename.toLowerCase() !== parentFolder.toLowerCase())
+                            continue;
+                    }
+                    files.push({ path, name: path.split('/').pop() ?? path });
+                }
+            }
+        }
+        else {
+            for (const pattern of patterns) {
+                const dir = pattern.replace(/\/$/, '');
+                try {
+                    const raw = await this.client.callTool(listTool.name, { directory: dir });
+                    const items = parseFileList(raw);
+                    for (const item of items) {
+                        const entry = typeof item === 'string' ? item : (item.path ?? item.filename ?? item.name);
+                        if (entry && entry.endsWith('.md')) {
+                            if (mapping.file_pattern) {
+                                const basename = (entry.split('/').pop() ?? entry).replace(/\.md$/, '');
+                                if (!matchGlob(mapping.file_pattern, basename))
+                                    continue;
+                            }
+                            if (mapping.name_match === 'folder') {
+                                const basename = (entry.split('/').pop() ?? entry).replace(/\.md$/, '');
+                                const parentFolder = dir.split('/').pop() ?? dir;
+                                if (basename.toLowerCase() !== parentFolder.toLowerCase())
+                                    continue;
+                            }
+                            const filename = entry.split('/').pop() ?? entry;
+                            files.push({ path: `${dir}/${filename}`, name: filename });
+                        }
+                    }
+                }
+                catch {
+                    // skip inaccessible directories
+                }
+            }
+        }
+        return files;
+    }
+    /**
+     * Extract one file via LLM.
+     */
+    async extractOne(file, mapping, onProgress) {
+        // Use explicit tool name from mapping, or fall back to heuristic matching
+        const tools = this.client.getTools();
+        const readTool = mapping.read_tool
+            ? tools.find(t => t.name === mapping.read_tool)
+            : tools.find(t => (t.name.includes('get') || t.name.includes('read')) &&
+                (t.name.includes('vault') || t.name.includes('note'))) ?? tools.find(t => (t.name.includes('get') || t.name.includes('read')) &&
+                t.name.includes('file') &&
+                !t.name.includes('active'));
+        if (!readTool) {
+            onProgress?.(`    Skip ${file.name}: no read tool found`);
+            return null;
+        }
+        let content;
+        try {
+            content = await this.client.callTool(readTool.name, { filename: file.path });
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            onProgress?.(`    Read error on ${file.name}: ${msg}`);
+            return null;
+        }
+        if (!content || content.length < 10) {
+            onProgress?.(`    Skip ${file.name}: empty or too short (${content?.length ?? 0} chars)`);
+            return null;
+        }
+        // Get schema for extraction
+        const schema = this.schemaRegistry.getSchema(mapping.entity_type);
+        try {
+            // Get cross-document context from GraphRAG if available
+            let graphragContext;
+            if (this.graphrag) {
+                const entityName = file.name.replace(/\.md$/, '');
+                const ctx = this.graphrag.getEntityContext(entityName, mapping.entity_type, content);
+                if (ctx.formattedContext) {
+                    graphragContext = ctx.formattedContext;
+                }
+            }
+            const frontmatter = await llmExtract(content, mapping.entity_type, schema, graphragContext);
+            // Generate entity_id from extracted name/title or filename
+            const nameField = frontmatter.name ?? frontmatter.title ?? file.name.replace(/\.md$/, '');
+            const entityId = slugify(String(nameField));
+            frontmatter.entity_type = mapping.entity_type;
+            frontmatter.entity_id = entityId;
+            return {
+                entity_type: mapping.entity_type,
+                entity_id: entityId,
+                target_repo: mapping.target_repo,
+                frontmatter,
+                content: '',
+                source_name: this.sourceConfig.name,
+                source_ref: `${this.sourceConfig.name}:${file.path}`,
+                confidence: 0.7,
+                ...(mapping.write_mode ? { write_mode: mapping.write_mode } : {}),
+                ...(mapping.co_locate ? { co_locate: mapping.co_locate } : {}),
+            };
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            onProgress?.(`    LLM error on ${file.name}: ${msg}`);
+            return null;
+        }
+    }
+    /**
+     * Extract all files for one mapping (with concurrency limit).
+     */
+    async extract(mapping, onProgress) {
+        if (mapping.extraction_mode !== 'unstructured')
+            return [];
+        const log = onProgress ?? (() => { });
+        const files = await this.discover(mapping);
+        log(`    Found ${files.length} files for LLM extraction`);
+        const results = [];
+        // Process in batches
+        for (let i = 0; i < files.length; i += CONCURRENCY_LIMIT) {
+            const batch = files.slice(i, i + CONCURRENCY_LIMIT);
+            const batchResults = await Promise.all(batch.map(file => this.extractOne(file, mapping, onProgress)));
+            for (const result of batchResults) {
+                if (result)
+                    results.push(result);
+            }
+        }
+        return results;
+    }
+}
+function tryParseJSON(raw) {
+    try {
+        return JSON.parse(raw);
+    }
+    catch {
+        return raw;
+    }
+}
+/** Parse an MCP file list response, handling both arrays and wrapped objects. */
+function parseFileList(raw) {
+    const parsed = tryParseJSON(raw);
+    if (Array.isArray(parsed))
+        return parsed;
+    const items = parsed?.files ?? parsed?.data ?? parsed?.results ?? parsed?.items;
+    return Array.isArray(items) ? items : [];
+}
+//# sourceMappingURL=unstructured-extractor.js.map

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@@ -0,0 +1 @@
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package/dist/services/vector-service.d.ts

@@ -69,6 +69,17 @@ export declare class VectorService {
     private generateEmbedding;
     private generateEmbeddingsBatch;
 }
+/**
+ * Index (or re-index) all entities across workspace repos into LanceDB.
+ * Standalone function — does not require a WorkspaceManager instance.
+ * Used by `join`, `commit`, and other CLI commands that land entities on disk.
+ *
+ * @returns Total number of entities indexed.
+ */
+export declare function reindexWorkspace(workspacePath: string, repos: Array<{
+    name: string;
+    path: string;
+}>, onProgress?: (msg: string) => void): Promise<number>;
 /**
  * Build a text representation of an entity for FTS/embedding.
  * Combines entity type, key frontmatter fields, and markdown body.

package/dist/services/vector-service.js

@@ -235,6 +235,48 @@ export class VectorService {
         return all;
     }
 }
+// ─── Standalone reindex ──────────────────────────────────────────────────────
+/**
+ * Index (or re-index) all entities across workspace repos into LanceDB.
+ * Standalone function — does not require a WorkspaceManager instance.
+ * Used by `join`, `commit`, and other CLI commands that land entities on disk.
+ *
+ * @returns Total number of entities indexed.
+ */
+export async function reindexWorkspace(workspacePath, repos, onProgress) {
+    const { loadUserConfig } = await import('../core/user-config.js');
+    const { BaseGraphManager } = await import('../core/graph.js');
+    const { homedir } = await import('os');
+    const userConfig = loadUserConfig();
+    const dbPath = userConfig.vector_db_path || join(homedir(), '.studiograph', 'vector');
+    const vectorService = new VectorService(dbPath, userConfig.voyage_api_key);
+    await vectorService.init();
+    const log = onProgress ?? (() => { });
+    let total = 0;
+    for (const repo of repos) {
+        const repoPath = join(workspacePath, repo.path);
+        if (!existsSync(repoPath))
+            continue;
+        try {
+            const graph = new BaseGraphManager({
+                repoPath,
+                repoName: repo.name,
+                gitUser: { id: 'reindex', name: 'reindex', email: 'reindex@studiograph.local' },
+            });
+            const entities = graph.list();
+            if (entities.length > 0) {
+                await vectorService.upsertMany(repo.name, entities);
+                total += entities.length;
+            }
+            vectorService.setLastIndexedTime(repo.name);
+            log(`  Indexed ${repo.name}: ${entities.length} entities`);
+        }
+        catch (err) {
+            log(`  Failed to index ${repo.name}: ${err instanceof Error ? err.message : 'unknown'}`);
+        }
+    }
+    return total;
+}
 // ─── Helpers ─────────────────────────────────────────────────────────────────
 /**
  * Build a text representation of an entity for FTS/embedding.

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

@@ -1 +1 @@
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package/dist/utils/git.d.ts

@@ -3,24 +3,51 @@
  * Extracted so tests can mock them without mocking the built-in child_process.
  */
 export type PullResult = 'updated' | 'up-to-date' | 'conflict';
-export type PushResult = 'pushed' | 'nothing-to-push';
+export type PushResult = 'pushed' | 'nothing-to-push' | 'rejected';
+export interface GitPullOptions {
+    /** When true (default), abort the rebase on conflict to leave repo clean.
+     *  Set to false to leave the rebase in progress so a resolver can work on it. */
+    abortOnConflict?: boolean;
+}
 /**
  * Pull the latest changes in a local git repo.
+ * Uses --rebase to automatically handle divergent branches
+ * (replays local commits on top of remote changes).
+ * Auto-stashes uncommitted changes before pulling and restores them after.
  * Returns 'updated', 'up-to-date', or 'conflict'.
  * Throws on hard errors (no remote, auth failure, etc.).
  */
-export declare function gitPull(repoPath: string): PullResult;
+export declare function gitPull(repoPath: string, opts?: GitPullOptions): PullResult;
 /**
  * Push local commits in a git repo to its remote.
- * Returns 'pushed' or 'nothing-to-push'.
- * Throws on errors (no remote, auth failure, etc.).
+ * Returns 'pushed', 'nothing-to-push', or 'rejected' (remote has newer commits).
+ * Throws on hard errors (no remote, auth failure, etc.).
  */
 export declare function gitPush(repoPath: string): PushResult;
+/**
+ * Pop the most recent stash entry, if any.
+ * Safe to call even if the stash is empty.
+ */
+export declare function gitStashPop(repoPath: string): void;
+/**
+ * Check if a git repo has uncommitted changes (staged or unstaged).
+ * Returns true if the working tree is dirty.
+ */
+export declare function gitHasUncommittedChanges(repoPath: string): boolean;
+/**
+ * Check if a directory is a git repository.
+ */
+export declare function isGitRepo(repoPath: string): boolean;
 /**
  * Clone a remote repository to a local path.
  * Throws if the git command fails.
  */
 export declare function gitClone(remoteUrl: string, localPath: string): void;
+/**
+ * Check if a git repo is currently in a rebase state.
+ * Looks for .git/rebase-merge/ or .git/rebase-apply/ directories.
+ */
+export declare function isInRebase(repoPath: string): boolean;
 /**
  * Read a git config value.
  * Returns undefined if the key is not set.

package/dist/utils/git.js

@@ -3,27 +3,51 @@
  * Extracted so tests can mock them without mocking the built-in child_process.
  */
 import { execSync, spawnSync } from 'child_process';
+import { existsSync } from 'fs';
+import { join } from 'path';
 /**
  * Pull the latest changes in a local git repo.
+ * Uses --rebase to automatically handle divergent branches
+ * (replays local commits on top of remote changes).
+ * Auto-stashes uncommitted changes before pulling and restores them after.
  * Returns 'updated', 'up-to-date', or 'conflict'.
  * Throws on hard errors (no remote, auth failure, etc.).
  */
-export function gitPull(repoPath) {
-    const result = spawnSync('git', ['pull'], { cwd: repoPath, encoding: 'utf-8' });
+export function gitPull(repoPath, opts) {
+    const abortOnConflict = opts?.abortOnConflict ?? true;
+    // Auto-stash if the working tree is dirty (rebase refuses to run otherwise)
+    const dirty = gitHasUncommittedChanges(repoPath);
+    if (dirty) {
+        spawnSync('git', ['stash', '--include-untracked'], { cwd: repoPath, encoding: 'utf-8' });
+    }
+    const result = spawnSync('git', ['pull', '--rebase'], { cwd: repoPath, encoding: 'utf-8' });
     if (result.status === 0) {
+        if (dirty)
+            spawnSync('git', ['stash', 'pop'], { cwd: repoPath, encoding: 'utf-8' });
         const output = result.stdout + result.stderr;
-        return output.toLowerCase().includes('already up to date') ? 'up-to-date' : 'updated';
+        return output.toLowerCase().includes('already up to date') ||
+            output.toLowerCase().includes('is up to date')
+            ? 'up-to-date'
+            : 'updated';
     }
     const combined = result.stdout + result.stderr;
-    if (combined.includes('CONFLICT') || combined.includes('Automatic merge failed')) {
+    if (combined.includes('CONFLICT') || combined.includes('could not apply')) {
+        if (abortOnConflict) {
+            spawnSync('git', ['rebase', '--abort'], { cwd: repoPath, encoding: 'utf-8' });
+            if (dirty)
+                spawnSync('git', ['stash', 'pop'], { cwd: repoPath, encoding: 'utf-8' });
+        }
+        // When !abortOnConflict, stash stays parked — resolver will pop after resolution
         return 'conflict';
     }
+    if (dirty)
+        spawnSync('git', ['stash', 'pop'], { cwd: repoPath, encoding: 'utf-8' });
     throw new Error((result.stderr || result.stdout || `git pull failed with exit ${result.status}`).trim());
 }
 /**
  * Push local commits in a git repo to its remote.
- * Returns 'pushed' or 'nothing-to-push'.
- * Throws on errors (no remote, auth failure, etc.).
+ * Returns 'pushed', 'nothing-to-push', or 'rejected' (remote has newer commits).
+ * Throws on hard errors (no remote, auth failure, etc.).
  */
 export function gitPush(repoPath) {
     const result = spawnSync('git', ['push'], { cwd: repoPath, encoding: 'utf-8' });
@@ -31,7 +55,33 @@ export function gitPush(repoPath) {
         const combined = result.stdout + result.stderr;
         return combined.includes('Everything up-to-date') ? 'nothing-to-push' : 'pushed';
     }
-    throw new Error((result.stderr || result.stdout || `git push failed with exit ${result.status}`).trim());
+    const combined = result.stdout + result.stderr;
+    if (combined.includes('non-fast-forward') || combined.includes('fetch first') || combined.includes('rejected')) {
+        return 'rejected';
+    }
+    throw new Error((combined || `git push failed with exit ${result.status}`).trim());
+}
+/**
+ * Pop the most recent stash entry, if any.
+ * Safe to call even if the stash is empty.
+ */
+export function gitStashPop(repoPath) {
+    spawnSync('git', ['stash', 'pop'], { cwd: repoPath, encoding: 'utf-8' });
+}
+/**
+ * Check if a git repo has uncommitted changes (staged or unstaged).
+ * Returns true if the working tree is dirty.
+ */
+export function gitHasUncommittedChanges(repoPath) {
+    const result = spawnSync('git', ['status', '--porcelain'], { cwd: repoPath, encoding: 'utf-8' });
+    return result.status === 0 && result.stdout.trim().length > 0;
+}
+/**
+ * Check if a directory is a git repository.
+ */
+export function isGitRepo(repoPath) {
+    const result = spawnSync('git', ['rev-parse', '--git-dir'], { cwd: repoPath, encoding: 'utf-8' });
+    return result.status === 0;
 }
 /**
  * Clone a remote repository to a local path.
@@ -40,6 +90,14 @@ export function gitPush(repoPath) {
 export function gitClone(remoteUrl, localPath) {
     execSync(`git clone "${remoteUrl}" "${localPath}"`, { stdio: 'pipe' });
 }
+/**
+ * Check if a git repo is currently in a rebase state.
+ * Looks for .git/rebase-merge/ or .git/rebase-apply/ directories.
+ */
+export function isInRebase(repoPath) {
+    return existsSync(join(repoPath, '.git', 'rebase-merge')) ||
+        existsSync(join(repoPath, '.git', 'rebase-apply'));
+}
 /**
  * Read a git config value.
  * Returns undefined if the key is not set.

package/dist/utils/git.js.map

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package/dist/utils/merge-resolver.d.ts

@@ -0,0 +1,60 @@
+/**
+ * Merge conflict resolution for markdown entity files.
+ *
+ * When git rebase hits a conflict, this module:
+ *   1. Classifies conflicted files by type (content, delete/modify, both-added, both-deleted)
+ *   2. Resolves delete conflicts automatically (no LLM needed)
+ *   3. For content conflicts, extracts ours/theirs versions from conflict markers
+ *   4. Asks an LLM to produce a merged version
+ *   5. Writes the merged content and stages the file
+ *   6. Continues the rebase
+ *
+ * Falls back gracefully if no API key is available (delete conflicts still resolve).
+ */
+export type ConflictType = 'content' | 'delete-modify' | 'modify-delete' | 'both-added' | 'both-deleted';
+export interface ConflictFile {
+    file: string;
+    type: ConflictType;
+}
+export interface MergeResolution {
+    file: string;
+    resolved: boolean;
+    summary?: string;
+}
+export interface ResolveResult {
+    success: boolean;
+    resolutions: MergeResolution[];
+}
+/**
+ * Classify unmerged files by parsing `git status --porcelain`.
+ * Returns typed conflict entries instead of bare file paths.
+ *
+ * Porcelain status codes for unmerged:
+ *   UU = both modified (content conflict)
+ *   DU = deleted by us, modified by them (during rebase: remote deleted, local modified)
+ *   UD = modified by us, deleted by them (during rebase: local deleted, remote modified)
+ *   AA = both added
+ *   DD = both deleted
+ */
+export declare function classifyConflicts(repoPath: string): ConflictFile[];
+/**
+ * Resolve a delete/modify or both-deleted conflict by accepting deletion.
+ * For entity folders (containing main.md), cleans up the parent if empty.
+ */
+export declare function resolveDeleteConflict(repoPath: string, conflict: ConflictFile): MergeResolution;
+/**
+ * Attempt to resolve all conflicts in a repo mid-rebase.
+ * The repo should be in a conflicted rebase state (not yet aborted).
+ * Returns success=true if all conflicts were resolved and rebase continued.
+ *
+ * Delete conflicts are resolved without an API key.
+ * Content conflicts require an LLM (API key).
+ */
+export declare function resolveConflicts(repoPath: string, onProgress?: (msg: string) => void): Promise<ResolveResult>;
+/**
+ * Extract ours and theirs versions from git conflict markers.
+ */
+export declare function extractConflictVersions(content: string): {
+    ours: string | null;
+    theirs: string | null;
+};