kiri-mcp-server 0.13.0 → 0.16.0

package/dist/src/indexer/cochange.d.ts

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+/**
+ * Co-change Graph Extraction (Phase 4: Graph Layer)
+ *
+ * This module extracts co-change relationships from git commit history.
+ * Files that frequently change together in commits have higher co-change scores.
+ *
+ * Invariants (from Alloy/TLA+ specs):
+ * - CC1: Canonical ordering (file1 < file2 lexicographically)
+ * - CC2: Both files exist in the file table
+ * - CC3: Positive weight (cochange_count > 0)
+ * - CC4: Idempotent commit processing
+ *
+ * Metrics computed:
+ * - cochange_count: Number of commits where both files changed together
+ * - confidence: Jaccard similarity = |A ∩ B| / |A ∪ B|
+ */
+import type { DuckDBClient } from "../shared/duckdb.js";
+/**
+ * Configuration for co-change extraction
+ */
+export interface CochangeConfig {
+    /** Maximum number of commits to analyze (default: 1000) */
+    maxCommits: number;
+    /** Minimum co-change count to persist (default: 2) */
+    minCochangeCount: number;
+    /** Maximum files per commit to avoid mega-commits (default: 50) */
+    maxFilesPerCommit: number;
+    /** Only consider commits within this many days (default: 365) */
+    maxAgeDays: number;
+}
+/**
+ * Parsed commit from git log
+ */
+interface GitCommit {
+    hash: string;
+    files: string[];
+    timestamp: Date;
+}
+/**
+ * Create canonical pair ensuring file1 < file2 (CC1)
+ * Uses lexicographic comparison for deterministic ordering.
+ */
+export declare function canonicalPair(file1: string, file2: string): [string, string];
+/**
+ * Generate all unique pairs from a set of files.
+ * Returns pairs in canonical order (file1 < file2).
+ */
+export declare function generatePairs(files: string[]): [string, string][];
+/**
+ * Extract commits from git log.
+ * Returns commits with their changed files.
+ */
+export declare function extractCommitsFromGit(repoPath: string, config: CochangeConfig): GitCommit[];
+/**
+ * Compute co-change graph from git history.
+ * Main entry point for co-change extraction.
+ *
+ * @param db - DuckDB client
+ * @param repoId - Repository ID
+ * @param repoPath - Path to git repository
+ * @param config - Optional configuration
+ */
+export declare function computeCochangeGraph(db: DuckDBClient, repoId: number, repoPath: string, config?: Partial<CochangeConfig>): Promise<{
+    processedCommits: number;
+    edges: number;
+    prunedEdges: number;
+}>;
+/**
+ * Incremental co-change update for new commits.
+ * Called during watch mode or incremental indexing.
+ *
+ * @param db - DuckDB client
+ * @param repoId - Repository ID
+ * @param repoPath - Path to git repository
+ * @param sinceCommit - Only process commits after this one
+ */
+export declare function incrementalCochangeUpdate(db: DuckDBClient, repoId: number, repoPath: string, sinceCommit?: string): Promise<{
+    processedCommits: number;
+}>;
+/**
+ * Remove co-change edges involving a deleted file.
+ * Called when files are removed from the index.
+ *
+ * Maintains CC2 invariant (both files exist).
+ */
+export declare function removeFileCochange(db: DuckDBClient, repoId: number, filePath: string): Promise<number>;
+/**
+ * Get co-change neighbors for a file.
+ * Returns files that frequently change together with the target file.
+ */
+export declare function getCochangeNeighbors(db: DuckDBClient, repoId: number, filePath: string, limit?: number): Promise<{
+    path: string;
+    count: number;
+    confidence: number;
+}[]>;
+export {};
+//# sourceMappingURL=cochange.d.ts.map

package/dist/src/indexer/cochange.d.ts.map

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package/dist/src/indexer/cochange.js

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+/**
+ * Co-change Graph Extraction (Phase 4: Graph Layer)
+ *
+ * This module extracts co-change relationships from git commit history.
+ * Files that frequently change together in commits have higher co-change scores.
+ *
+ * Invariants (from Alloy/TLA+ specs):
+ * - CC1: Canonical ordering (file1 < file2 lexicographically)
+ * - CC2: Both files exist in the file table
+ * - CC3: Positive weight (cochange_count > 0)
+ * - CC4: Idempotent commit processing
+ *
+ * Metrics computed:
+ * - cochange_count: Number of commits where both files changed together
+ * - confidence: Jaccard similarity = |A ∩ B| / |A ∪ B|
+ */
+import { execSync } from "node:child_process";
+const DEFAULT_CONFIG = {
+    maxCommits: 1000,
+    minCochangeCount: 2,
+    maxFilesPerCommit: 50,
+    maxAgeDays: 365,
+};
+/**
+ * Create canonical pair ensuring file1 < file2 (CC1)
+ * Uses lexicographic comparison for deterministic ordering.
+ */
+export function canonicalPair(file1, file2) {
+    return file1 < file2 ? [file1, file2] : [file2, file1];
+}
+/**
+ * Generate all unique pairs from a set of files.
+ * Returns pairs in canonical order (file1 < file2).
+ */
+export function generatePairs(files) {
+    const pairs = [];
+    const sorted = [...files].sort();
+    for (let i = 0; i < sorted.length; i++) {
+        for (let j = i + 1; j < sorted.length; j++) {
+            const f1 = sorted[i];
+            const f2 = sorted[j];
+            if (f1 !== undefined && f2 !== undefined) {
+                pairs.push([f1, f2]);
+            }
+        }
+    }
+    return pairs;
+}
+/**
+ * Extract commits from git log.
+ * Returns commits with their changed files.
+ */
+export function extractCommitsFromGit(repoPath, config) {
+    const commits = [];
+    try {
+        // Get commit hashes with timestamps
+        // Format: hash|timestamp (ISO 8601)
+        const sinceDate = new Date();
+        sinceDate.setDate(sinceDate.getDate() - config.maxAgeDays);
+        const sinceArg = sinceDate.toISOString().split("T")[0];
+        const logOutput = execSync(`git log --format="%H|%aI" --since="${sinceArg}" -n ${config.maxCommits}`, {
+            cwd: repoPath,
+            encoding: "utf-8",
+            maxBuffer: 50 * 1024 * 1024, // 50MB buffer for large repos
+        });
+        const commitLines = logOutput.trim().split("\n").filter(Boolean);
+        for (const line of commitLines) {
+            const [hash, timestampStr] = line.split("|");
+            if (!hash || !timestampStr)
+                continue;
+            // Get files changed in this commit
+            const filesOutput = execSync(`git diff-tree --no-commit-id --name-only -r ${hash}`, {
+                cwd: repoPath,
+                encoding: "utf-8",
+                maxBuffer: 10 * 1024 * 1024,
+            });
+            const files = filesOutput
+                .trim()
+                .split("\n")
+                .filter(Boolean)
+                .filter((f) => !f.startsWith(".git/"));
+            // Skip mega-commits (likely auto-generated or initial commits)
+            if (files.length > config.maxFilesPerCommit) {
+                continue;
+            }
+            // Skip single-file commits (no pairs possible)
+            if (files.length < 2) {
+                continue;
+            }
+            commits.push({
+                hash,
+                files,
+                timestamp: new Date(timestampStr),
+            });
+        }
+    }
+    catch (error) {
+        console.warn("[Cochange] Failed to extract git history:", error);
+    }
+    return commits;
+}
+/**
+ * Check if a commit has already been processed (CC4: Idempotent)
+ */
+async function isCommitProcessed(db, repoId, commitHash) {
+    const result = await db.all(`SELECT COUNT(*) as count FROM processed_commits
+     WHERE repo_id = ? AND commit_hash = ?`, [repoId, commitHash]);
+    return (result[0]?.count ?? 0) > 0;
+}
+/**
+ * Mark a commit as processed (CC4: Idempotent)
+ */
+async function markCommitProcessed(db, repoId, commitHash) {
+    await db.run(`INSERT INTO processed_commits (repo_id, commit_hash, processed_at)
+     VALUES (?, ?, CURRENT_TIMESTAMP)
+     ON CONFLICT DO NOTHING`, [repoId, commitHash]);
+}
+/**
+ * Get set of indexed files for a repo (CC2: Both files exist)
+ */
+async function getIndexedFiles(db, repoId) {
+    const files = await db.all(`SELECT path FROM file WHERE repo_id = ?`, [repoId]);
+    return new Set(files.map((f) => f.path));
+}
+/**
+ * Update co-change counts for a single commit.
+ * Creates pairs for all changed files and increments counts.
+ */
+async function processCommitCochange(db, repoId, commit, indexedFiles, fileChangeCounts) {
+    // Filter to only indexed files (CC2)
+    const validFiles = commit.files.filter((f) => indexedFiles.has(f));
+    if (validFiles.length < 2) {
+        return; // Need at least 2 files for pairs
+    }
+    // Update file change counts
+    for (const file of validFiles) {
+        fileChangeCounts.set(file, (fileChangeCounts.get(file) ?? 0) + 1);
+    }
+    // Generate all pairs (CC1: canonical ordering)
+    const pairs = generatePairs(validFiles);
+    // Update co-change counts
+    for (const [file1, file2] of pairs) {
+        await db.run(`INSERT INTO cochange (repo_id, file1, file2, cochange_count, last_commit, last_cochange_at)
+       VALUES (?, ?, ?, 1, ?, CURRENT_TIMESTAMP)
+       ON CONFLICT (repo_id, file1, file2) DO UPDATE SET
+         cochange_count = cochange_count + 1,
+         last_commit = excluded.last_commit,
+         last_cochange_at = excluded.last_cochange_at`, [repoId, file1, file2, commit.hash]);
+    }
+}
+/**
+ * Calculate Jaccard confidence for all co-change edges.
+ * confidence = cochange_count / (changes_file1 + changes_file2 - cochange_count)
+ *
+ * This is run after all commits are processed.
+ */
+async function updateJaccardConfidence(db, repoId, fileChangeCounts) {
+    // Get all co-change edges
+    const edges = await db.all(`SELECT file1, file2, cochange_count FROM cochange WHERE repo_id = ?`, [repoId]);
+    for (const edge of edges) {
+        const count1 = fileChangeCounts.get(edge.file1) ?? 0;
+        const count2 = fileChangeCounts.get(edge.file2) ?? 0;
+        // Jaccard = intersection / union
+        // intersection = cochange_count
+        // union = changes_file1 + changes_file2 - cochange_count
+        const union = count1 + count2 - edge.cochange_count;
+        const confidence = union > 0 ? edge.cochange_count / union : 0;
+        await db.run(`UPDATE cochange SET confidence = ?
+       WHERE repo_id = ? AND file1 = ? AND file2 = ?`, [confidence, repoId, edge.file1, edge.file2]);
+    }
+}
+/**
+ * Prune co-change edges below minimum threshold (CC3: Positive weight)
+ */
+async function pruneWeakEdges(db, repoId, minCochangeCount) {
+    // Count rows to be deleted first
+    const countResult = await db.all(`SELECT COUNT(*) as count FROM cochange
+     WHERE repo_id = ? AND cochange_count < ?`, [repoId, minCochangeCount]);
+    const toDelete = countResult[0]?.count ?? 0;
+    // Delete the rows
+    await db.run(`DELETE FROM cochange
+     WHERE repo_id = ? AND cochange_count < ?`, [repoId, minCochangeCount]);
+    return toDelete;
+}
+/**
+ * Compute co-change graph from git history.
+ * Main entry point for co-change extraction.
+ *
+ * @param db - DuckDB client
+ * @param repoId - Repository ID
+ * @param repoPath - Path to git repository
+ * @param config - Optional configuration
+ */
+export async function computeCochangeGraph(db, repoId, repoPath, config = {}) {
+    const cfg = { ...DEFAULT_CONFIG, ...config };
+    console.info(`[Cochange] Computing co-change graph for repo ${repoId}...`);
+    // Get indexed files (CC2)
+    const indexedFiles = await getIndexedFiles(db, repoId);
+    if (indexedFiles.size === 0) {
+        console.info("[Cochange] No indexed files, skipping");
+        return { processedCommits: 0, edges: 0, prunedEdges: 0 };
+    }
+    // Extract commits from git
+    const commits = extractCommitsFromGit(repoPath, cfg);
+    console.info(`[Cochange] Found ${commits.length} commits to analyze`);
+    // Track file change counts for Jaccard calculation
+    const fileChangeCounts = new Map();
+    let processedCount = 0;
+    // Process each commit
+    for (const commit of commits) {
+        // Check idempotency (CC4)
+        const alreadyProcessed = await isCommitProcessed(db, repoId, commit.hash);
+        if (alreadyProcessed) {
+            continue;
+        }
+        // Process co-change pairs
+        await processCommitCochange(db, repoId, commit, indexedFiles, fileChangeCounts);
+        // Mark as processed (CC4)
+        await markCommitProcessed(db, repoId, commit.hash);
+        processedCount++;
+    }
+    console.info(`[Cochange] Processed ${processedCount} new commits`);
+    // Update Jaccard confidence scores only if we processed new commits
+    // Skip when processedCount is 0 to avoid zeroing existing confidence values
+    if (processedCount > 0) {
+        await updateJaccardConfidence(db, repoId, fileChangeCounts);
+    }
+    // Prune weak edges (CC3)
+    const prunedCount = await pruneWeakEdges(db, repoId, cfg.minCochangeCount);
+    // Get final edge count
+    const edgeCount = await db.all(`SELECT COUNT(*) as count FROM cochange WHERE repo_id = ?`, [repoId]);
+    console.info(`[Cochange] Completed: ${edgeCount[0]?.count ?? 0} edges, ${prunedCount} pruned`);
+    return {
+        processedCommits: processedCount,
+        edges: edgeCount[0]?.count ?? 0,
+        prunedEdges: prunedCount,
+    };
+}
+/**
+ * Incremental co-change update for new commits.
+ * Called during watch mode or incremental indexing.
+ *
+ * @param db - DuckDB client
+ * @param repoId - Repository ID
+ * @param repoPath - Path to git repository
+ * @param sinceCommit - Only process commits after this one
+ */
+export async function incrementalCochangeUpdate(db, repoId, repoPath, sinceCommit) {
+    console.info(`[Cochange] Incremental update for repo ${repoId}...`);
+    const indexedFiles = await getIndexedFiles(db, repoId);
+    const fileChangeCounts = new Map();
+    // Build file change counts from existing data
+    const existingEdges = await db.all(`SELECT DISTINCT file1, file2 FROM cochange WHERE repo_id = ?`, [repoId]);
+    // Note: This is a simplified approximation. Full recalc would be more accurate.
+    for (const edge of existingEdges) {
+        fileChangeCounts.set(edge.file1, (fileChangeCounts.get(edge.file1) ?? 0) + 1);
+        fileChangeCounts.set(edge.file2, (fileChangeCounts.get(edge.file2) ?? 0) + 1);
+    }
+    // Extract recent commits
+    const cfg = { ...DEFAULT_CONFIG, maxCommits: 100, maxAgeDays: 30 };
+    const commits = extractCommitsFromGit(repoPath, cfg);
+    let processedCount = 0;
+    for (const commit of commits) {
+        // Skip if already processed
+        if (await isCommitProcessed(db, repoId, commit.hash)) {
+            continue;
+        }
+        // Skip if before sinceCommit (optimization)
+        if (sinceCommit && commit.hash === sinceCommit) {
+            break;
+        }
+        await processCommitCochange(db, repoId, commit, indexedFiles, fileChangeCounts);
+        await markCommitProcessed(db, repoId, commit.hash);
+        processedCount++;
+    }
+    // Update confidence scores
+    if (processedCount > 0) {
+        await updateJaccardConfidence(db, repoId, fileChangeCounts);
+    }
+    console.info(`[Cochange] Incremental update: ${processedCount} commits`);
+    return { processedCommits: processedCount };
+}
+/**
+ * Remove co-change edges involving a deleted file.
+ * Called when files are removed from the index.
+ *
+ * Maintains CC2 invariant (both files exist).
+ */
+export async function removeFileCochange(db, repoId, filePath) {
+    // Count rows to be deleted first
+    const countResult = await db.all(`SELECT COUNT(*) as count FROM cochange
+     WHERE repo_id = ? AND (file1 = ? OR file2 = ?)`, [repoId, filePath, filePath]);
+    const toDelete = countResult[0]?.count ?? 0;
+    // Delete the rows
+    await db.run(`DELETE FROM cochange
+     WHERE repo_id = ? AND (file1 = ? OR file2 = ?)`, [repoId, filePath, filePath]);
+    return toDelete;
+}
+/**
+ * Get co-change neighbors for a file.
+ * Returns files that frequently change together with the target file.
+ */
+export async function getCochangeNeighbors(db, repoId, filePath, limit = 10) {
+    // Query both directions (file can be in file1 or file2)
+    const results = await db.all(`SELECT
+       CASE WHEN file1 = ? THEN file2 ELSE file1 END as path,
+       cochange_count as count,
+       confidence
+     FROM cochange
+     WHERE repo_id = ? AND (file1 = ? OR file2 = ?)
+     ORDER BY cochange_count DESC, confidence DESC
+     LIMIT ?`, [filePath, repoId, filePath, filePath, limit]);
+    return results;
+}
+//# sourceMappingURL=cochange.js.map

package/dist/src/indexer/cochange.js.map

@@ -0,0 +1 @@
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package/dist/src/indexer/graph-metrics.d.ts

@@ -0,0 +1,68 @@
+/**
+ * Graph Metrics Computation (Phase 3.2: Graph Layer)
+ *
+ * This module computes graph centrality metrics from the dependency table
+ * and stores them in precomputed tables for fast query-time lookup.
+ *
+ * Invariants (from Alloy spec):
+ * - DG1: All path edges reference indexed files
+ * - DG2: No self-loops
+ * - DG4: Closure symmetry (outbound/inbound consistency)
+ *
+ * Metrics computed:
+ * - Degree centrality (inbound/outbound counts)
+ * - Importance score (PageRank-like)
+ * - Inbound closure (BFS up to depth 3)
+ */
+import type { DuckDBClient } from "../shared/duckdb.js";
+/**
+ * Configuration for graph metrics computation
+ */
+export interface GraphMetricsConfig {
+    /** Maximum BFS depth for inbound closure (default: 3) */
+    maxDepth: number;
+    /** PageRank damping factor (default: 0.85) */
+    dampingFactor: number;
+    /** Number of PageRank iterations (default: 10) */
+    iterations: number;
+}
+/**
+ * Compute all graph metrics for a repository.
+ * Called after dependency extraction during indexing.
+ *
+ * @param db - DuckDB client
+ * @param repoId - Repository ID
+ * @param config - Optional configuration
+ */
+export declare function computeGraphMetrics(db: DuckDBClient, repoId: number, config?: Partial<GraphMetricsConfig>): Promise<void>;
+/**
+ * Compute degree centrality (inbound and outbound counts).
+ *
+ * Uses SQL aggregation for efficiency.
+ */
+export declare function computeDegreeCentrality(db: DuckDBClient, repoId: number): Promise<void>;
+/**
+ * Precompute inbound closure using BFS up to maxDepth.
+ *
+ * Uses recursive CTE for efficient computation.
+ */
+export declare function precomputeInboundClosure(db: DuckDBClient, repoId: number, maxDepth: number): Promise<void>;
+/**
+ * Compute importance scores using PageRank-like algorithm.
+ *
+ * This is a simplified PageRank that:
+ * - Uses inbound edges for importance propagation
+ * - Runs for a fixed number of iterations
+ * - Normalizes scores to [0, 1]
+ */
+export declare function computeImportanceScores(db: DuckDBClient, repoId: number, dampingFactor: number, iterations: number): Promise<void>;
+/**
+ * Incrementally update graph metrics for changed files.
+ * Used during incremental indexing to avoid full recomputation.
+ *
+ * @param db - DuckDB client
+ * @param repoId - Repository ID
+ * @param changedPaths - Paths that were added, modified, or removed
+ */
+export declare function incrementalGraphUpdate(db: DuckDBClient, repoId: number, changedPaths: string[]): Promise<void>;
+//# sourceMappingURL=graph-metrics.d.ts.map

package/dist/src/indexer/graph-metrics.d.ts.map

@@ -0,0 +1 @@
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