composto-ai 0.4.0 → 0.6.0

package/dist/mcp/server.js

@@ -1558,7 +1558,25 @@ function openDatabase(path) {
 }
 
 // src/memory/schema.ts
-var CURRENT_VERSION = 1;
+var CURRENT_VERSION = 3;
+var V2_SQL = `
+CREATE INDEX IF NOT EXISTS idx_ft_file_commit ON file_touches(file_path, commit_sha);
+`;
+var V3_SQL = `
+CREATE TABLE IF NOT EXISTS hook_invocations (
+  id              INTEGER PRIMARY KEY AUTOINCREMENT,
+  timestamp       INTEGER NOT NULL,
+  platform        TEXT NOT NULL,
+  event           TEXT NOT NULL,
+  file_path       TEXT,
+  verdict         TEXT,
+  score           REAL,
+  confidence      REAL,
+  latency_ms      INTEGER NOT NULL,
+  cache_hit       INTEGER NOT NULL
+);
+CREATE INDEX IF NOT EXISTS idx_hi_timestamp ON hook_invocations(timestamp);
+`;
 var V1_SQL = `
 CREATE TABLE IF NOT EXISTS index_state (
   key   TEXT PRIMARY KEY,
@@ -1646,7 +1664,9 @@ function runMigrations(db) {
   if (current >= CURRENT_VERSION) return;
   db.exec("BEGIN");
   try {
-    db.exec(V1_SQL);
+    if (current < 1) db.exec(V1_SQL);
+    if (current < 2) db.exec(V2_SQL);
+    if (current < 3) db.exec(V3_SQL);
     db.pragma(`user_version = ${CURRENT_VERSION}`);
     db.exec("COMMIT");
   } catch (err) {
@@ -1788,13 +1808,19 @@ function computeRevertMatch(db, filePath) {
   };
 }
 
+// src/memory/signals/db-clock.ts
+function getDbMaxTimestamp(db) {
+  const row = db.prepare("SELECT MAX(timestamp) AS ts FROM commits").get();
+  return row?.ts ?? null;
+}
+
 // src/memory/signals/hotspot.ts
 var WINDOW_SECONDS = 90 * 86400;
 var SATURATION_TOUCHES = 30;
 var FALLBACK_PRECISION2 = 0.3;
 function computeHotspot(db, filePath) {
-  const now = Math.floor(Date.now() / 1e3);
-  const lowerBound = now - WINDOW_SECONDS;
+  const anchor = getDbMaxTimestamp(db) ?? Math.floor(Date.now() / 1e3);
+  const lowerBound = anchor - WINDOW_SECONDS;
   const row = db.prepare(`
       SELECT COUNT(*) AS n
       FROM file_touches ft
@@ -1852,38 +1878,12 @@ function computeFixRatio(db, filePath) {
   };
 }
 
-// src/memory/signals/coverage-decline.ts
-var FALLBACK_PRECISION4 = 0.3;
-function computeCoverageDecline(db, repoPath, filePath) {
-  const cal = getCalibration(db, "coverage_decline", FALLBACK_PRECISION4);
-  let strength = 0;
-  try {
-    const entries = getGitLog(repoPath, 200);
-    const trends = {
-      hotspots: detectHotspots(entries, { threshold: 10, fixRatioThreshold: 0.5 }),
-      decaySignals: detectDecay(entries),
-      inconsistencies: detectInconsistencies(entries)
-    };
-    const health = computeHealthFromTrends(filePath, trends);
-    if (health.coverageTrend === "down") strength = 1;
-  } catch {
-    strength = 0;
-  }
-  return {
-    type: "coverage_decline",
-    strength,
-    precision: cal.precision,
-    sample_size: cal.sampleSize,
-    evidence: []
-  };
-}
-
 // src/memory/signals/author-churn.ts
 var WINDOW_SECONDS2 = 90 * 86400;
 var INACTIVE_THRESHOLD = 5;
-var FALLBACK_PRECISION5 = 0.3;
+var FALLBACK_PRECISION4 = 0.3;
 function computeAuthorChurn(db, filePath) {
-  const cal = getCalibration(db, "author_churn", FALLBACK_PRECISION5);
+  const cal = getCalibration(db, "author_churn", FALLBACK_PRECISION4);
   const base = {
     type: "author_churn",
     precision: cal.precision,
@@ -1899,8 +1899,8 @@ function computeAuthorChurn(db, filePath) {
       LIMIT 1
     `).get(filePath);
   if (!lastTouch) return { ...base, strength: 0 };
-  const now = Math.floor(Date.now() / 1e3);
-  const lowerBound = now - WINDOW_SECONDS2;
+  const anchor = getDbMaxTimestamp(db) ?? Math.floor(Date.now() / 1e3);
+  const lowerBound = anchor - WINDOW_SECONDS2;
   const activity = db.prepare(`SELECT COUNT(*) AS n FROM commits WHERE author = ? AND timestamp >= ?`).get(lastTouch.author, lowerBound);
   let strength = 0;
   if (activity.n === 0) strength = 1;
@@ -1909,12 +1909,11 @@ function computeAuthorChurn(db, filePath) {
 }
 
 // src/memory/signals/index.ts
-function collectSignals(db, repoPath, filePath) {
+function collectSignals(db, _repoPath, filePath) {
   return [
     computeRevertMatch(db, filePath),
     computeHotspot(db, filePath),
     computeFixRatio(db, filePath),
-    computeCoverageDecline(db, repoPath, filePath),
     computeAuthorChurn(db, filePath)
   ];
 }
@@ -2245,6 +2244,24 @@ var MemoryAPI = class {
     });
     return this.bootstrapPromise;
   }
+  // bootstrapFromBoundary indexes only commits between fromSha and HEAD.
+  // Used by `composto index --since=YYYY-MM-DD` to bound work on huge repos.
+  // Pass fromSha=null to index the full history (same as bootstrapIfNeeded).
+  async bootstrapFromBoundary(fromSha) {
+    if (this.bootstrapPromise) return this.bootstrapPromise;
+    const head = revParseHead(this.repoPath);
+    const range = { from: fromSha, to: head };
+    this.bootstrapPromise = this.pool.runIngest({ dbPath: this.dbPath, repoPath: this.repoPath, range }).then(() => {
+      this.log.info("bootstrap_done", { through: range.to, from: range.from });
+    }).catch((err) => {
+      this.log.error("bootstrap_failed", { message: err.message });
+      this.failures.recordFailure("ingest_failure");
+      throw err;
+    }).finally(() => {
+      this.bootstrapPromise = null;
+    });
+    return this.bootstrapPromise;
+  }
   async blastradius(input) {
     const start = Date.now();
     if (this.failures.isDisabled()) {
@@ -2366,7 +2383,7 @@ var MemoryAPI = class {
 var ALL_EXTENSIONS = [".ts", ".tsx", ".js", ".jsx", ".mjs", ".py", ".go", ".rs"];
 var server = new McpServer({
   name: "composto",
-  version: "0.4.0"
+  version: "0.4.2"
 });
 server.tool(
   "composto_ir",

package/dist/memory/api.js

@@ -14,7 +14,25 @@ function openDatabase(path) {
 }
 
 // src/memory/schema.ts
-var CURRENT_VERSION = 1;
+var CURRENT_VERSION = 3;
+var V2_SQL = `
+CREATE INDEX IF NOT EXISTS idx_ft_file_commit ON file_touches(file_path, commit_sha);
+`;
+var V3_SQL = `
+CREATE TABLE IF NOT EXISTS hook_invocations (
+  id              INTEGER PRIMARY KEY AUTOINCREMENT,
+  timestamp       INTEGER NOT NULL,
+  platform        TEXT NOT NULL,
+  event           TEXT NOT NULL,
+  file_path       TEXT,
+  verdict         TEXT,
+  score           REAL,
+  confidence      REAL,
+  latency_ms      INTEGER NOT NULL,
+  cache_hit       INTEGER NOT NULL
+);
+CREATE INDEX IF NOT EXISTS idx_hi_timestamp ON hook_invocations(timestamp);
+`;
 var V1_SQL = `
 CREATE TABLE IF NOT EXISTS index_state (
   key   TEXT PRIMARY KEY,
@@ -102,7 +120,9 @@ function runMigrations(db) {
   if (current >= CURRENT_VERSION) return;
   db.exec("BEGIN");
   try {
-    db.exec(V1_SQL);
+    if (current < 1) db.exec(V1_SQL);
+    if (current < 2) db.exec(V2_SQL);
+    if (current < 3) db.exec(V3_SQL);
     db.pragma(`user_version = ${CURRENT_VERSION}`);
     db.exec("COMMIT");
   } catch (err) {
@@ -244,13 +264,19 @@ function computeRevertMatch(db, filePath) {
   };
 }
 
+// src/memory/signals/db-clock.ts
+function getDbMaxTimestamp(db) {
+  const row = db.prepare("SELECT MAX(timestamp) AS ts FROM commits").get();
+  return row?.ts ?? null;
+}
+
 // src/memory/signals/hotspot.ts
 var WINDOW_SECONDS = 90 * 86400;
 var SATURATION_TOUCHES = 30;
 var FALLBACK_PRECISION2 = 0.3;
 function computeHotspot(db, filePath) {
-  const now = Math.floor(Date.now() / 1e3);
-  const lowerBound = now - WINDOW_SECONDS;
+  const anchor = getDbMaxTimestamp(db) ?? Math.floor(Date.now() / 1e3);
+  const lowerBound = anchor - WINDOW_SECONDS;
   const row = db.prepare(`
       SELECT COUNT(*) AS n
       FROM file_touches ft
@@ -308,202 +334,12 @@ function computeFixRatio(db, filePath) {
   };
 }
 
-// src/trends/git-log-parser.ts
-import { execSync as execSync2 } from "child_process";
-var BUG_FIX_PATTERNS = [
-  /\bfix\b/i,
-  /\bbugfix\b/i,
-  /\bhotfix\b/i,
-  /\bpatch\b/i,
-  /\bresolve\b/i,
-  /\bbug\b/i
-];
-function isBugFixCommit(message) {
-  return BUG_FIX_PATTERNS.some((p) => p.test(message));
-}
-function parseGitLogOutput(output) {
-  const entries = [];
-  const lines = output.split("\n");
-  let i = 0;
-  while (i < lines.length) {
-    const line = lines[i].trim();
-    if (!line || !line.includes("|")) {
-      i++;
-      continue;
-    }
-    const [hash, author, date, ...messageParts] = line.split("|");
-    const message = messageParts.join("|");
-    const files = [];
-    i++;
-    while (i < lines.length && lines[i].trim() !== "" && !lines[i].includes("|")) {
-      const fileLine = lines[i].trim();
-      if (fileLine) files.push(fileLine);
-      i++;
-    }
-    entries.push({ hash, author, date, message, files });
-  }
-  return entries;
-}
-function getGitLog(repoPath, count = 100) {
-  try {
-    const output = execSync2(
-      `git log --format="%h|%an|%as|%s" --name-only -n ${count}`,
-      { cwd: repoPath, encoding: "utf-8", timeout: 1e4 }
-    );
-    return parseGitLogOutput(output);
-  } catch {
-    return [];
-  }
-}
-
-// src/trends/hotspot.ts
-function detectHotspots(entries, options) {
-  const fileStats = /* @__PURE__ */ new Map();
-  for (const entry of entries) {
-    const isFix = isBugFixCommit(entry.message);
-    for (const file of entry.files) {
-      const stats = fileStats.get(file) ?? { changes: 0, fixes: 0, authors: /* @__PURE__ */ new Set() };
-      stats.changes++;
-      if (isFix) stats.fixes++;
-      stats.authors.add(entry.author);
-      fileStats.set(file, stats);
-    }
-  }
-  const hotspots = [];
-  for (const [file, stats] of fileStats) {
-    const fixRatio = stats.changes > 0 ? stats.fixes / stats.changes : 0;
-    if (stats.changes >= options.threshold && fixRatio >= options.fixRatioThreshold) {
-      hotspots.push({
-        file,
-        changesInLast30Commits: stats.changes,
-        bugFixRatio: fixRatio,
-        authorCount: stats.authors.size
-      });
-    }
-  }
-  return hotspots.sort((a, b) => b.changesInLast30Commits - a.changesInLast30Commits);
-}
-
-// src/trends/decay.ts
-function detectDecay(entries) {
-  const fileChanges = /* @__PURE__ */ new Map();
-  for (const entry of entries) {
-    for (const file of entry.files) {
-      const changes = fileChanges.get(file) ?? [];
-      changes.push({ date: entry.date });
-      fileChanges.set(file, changes);
-    }
-  }
-  const signals = [];
-  for (const [file, changes] of fileChanges) {
-    if (changes.length < 4) continue;
-    const sorted = [...changes].sort((a, b) => a.date.localeCompare(b.date));
-    const firstDate = new Date(sorted[0].date).getTime();
-    const lastDate = new Date(sorted[sorted.length - 1].date).getTime();
-    const midDate = firstDate + (lastDate - firstDate) / 2;
-    const firstHalfCount = sorted.filter((c) => new Date(c.date).getTime() <= midDate).length;
-    const secondHalfCount = sorted.length - firstHalfCount;
-    if (secondHalfCount > firstHalfCount) {
-      signals.push({
-        file,
-        metric: "churn",
-        trend: "declining",
-        dataPoints: sorted.map((c, i) => ({ date: c.date, value: i + 1 }))
-      });
-    }
-  }
-  return signals;
-}
-
-// src/trends/inconsistency.ts
-function detectInconsistencies(entries, minAuthors = 3) {
-  const fileAuthors = /* @__PURE__ */ new Map();
-  for (const entry of entries) {
-    for (const file of entry.files) {
-      const authors = fileAuthors.get(file) ?? /* @__PURE__ */ new Map();
-      const commits = authors.get(entry.author) ?? [];
-      commits.push(entry.message);
-      authors.set(entry.author, commits);
-      fileAuthors.set(file, authors);
-    }
-  }
-  const inconsistencies = [];
-  for (const [file, authors] of fileAuthors) {
-    if (authors.size >= minAuthors) {
-      const patterns = Array.from(authors.entries()).map(([author, commits]) => ({
-        author,
-        style: categorizeStyle(commits)
-      }));
-      inconsistencies.push({ file, patterns });
-    }
-  }
-  return inconsistencies;
-}
-function categorizeStyle(commits) {
-  const types = commits.map((m) => {
-    if (m.match(/^fix/i)) return "fix";
-    if (m.match(/^feat/i)) return "feature";
-    if (m.match(/^refactor/i)) return "refactor";
-    return "other";
-  });
-  const primary = mode(types);
-  return `primarily ${primary} (${commits.length} commits)`;
-}
-function mode(arr) {
-  const counts = /* @__PURE__ */ new Map();
-  for (const item of arr) {
-    counts.set(item, (counts.get(item) ?? 0) + 1);
-  }
-  return Array.from(counts.entries()).sort((a, b) => b[1] - a[1])[0]?.[0] ?? "unknown";
-}
-
-// src/ir/health.ts
-function computeHealthFromTrends(file, trends) {
-  const hotspot = trends.hotspots.find((h) => h.file === file);
-  const decay = trends.decaySignals.find((d) => d.file === file);
-  const inconsistency = trends.inconsistencies.find((i) => i.file === file);
-  return {
-    churn: hotspot?.changesInLast30Commits ?? 0,
-    fixRatio: hotspot?.bugFixRatio ?? 0,
-    coverageTrend: decay?.trend === "declining" ? "down" : decay?.trend === "improving" ? "up" : "stable",
-    staleness: "",
-    authorCount: hotspot?.authorCount ?? 0,
-    consistency: inconsistency ? "low" : "high"
-  };
-}
-
-// src/memory/signals/coverage-decline.ts
-var FALLBACK_PRECISION4 = 0.3;
-function computeCoverageDecline(db, repoPath, filePath) {
-  const cal = getCalibration(db, "coverage_decline", FALLBACK_PRECISION4);
-  let strength = 0;
-  try {
-    const entries = getGitLog(repoPath, 200);
-    const trends = {
-      hotspots: detectHotspots(entries, { threshold: 10, fixRatioThreshold: 0.5 }),
-      decaySignals: detectDecay(entries),
-      inconsistencies: detectInconsistencies(entries)
-    };
-    const health = computeHealthFromTrends(filePath, trends);
-    if (health.coverageTrend === "down") strength = 1;
-  } catch {
-    strength = 0;
-  }
-  return {
-    type: "coverage_decline",
-    strength,
-    precision: cal.precision,
-    sample_size: cal.sampleSize,
-    evidence: []
-  };
-}
-
 // src/memory/signals/author-churn.ts
 var WINDOW_SECONDS2 = 90 * 86400;
 var INACTIVE_THRESHOLD = 5;
-var FALLBACK_PRECISION5 = 0.3;
+var FALLBACK_PRECISION4 = 0.3;
 function computeAuthorChurn(db, filePath) {
-  const cal = getCalibration(db, "author_churn", FALLBACK_PRECISION5);
+  const cal = getCalibration(db, "author_churn", FALLBACK_PRECISION4);
   const base = {
     type: "author_churn",
     precision: cal.precision,
@@ -519,8 +355,8 @@ function computeAuthorChurn(db, filePath) {
       LIMIT 1
     `).get(filePath);
   if (!lastTouch) return { ...base, strength: 0 };
-  const now = Math.floor(Date.now() / 1e3);
-  const lowerBound = now - WINDOW_SECONDS2;
+  const anchor = getDbMaxTimestamp(db) ?? Math.floor(Date.now() / 1e3);
+  const lowerBound = anchor - WINDOW_SECONDS2;
   const activity = db.prepare(`SELECT COUNT(*) AS n FROM commits WHERE author = ? AND timestamp >= ?`).get(lastTouch.author, lowerBound);
   let strength = 0;
   if (activity.n === 0) strength = 1;
@@ -529,12 +365,11 @@ function computeAuthorChurn(db, filePath) {
 }
 
 // src/memory/signals/index.ts
-function collectSignals(db, repoPath, filePath) {
+function collectSignals(db, _repoPath, filePath) {
   return [
     computeRevertMatch(db, filePath),
     computeHotspot(db, filePath),
     computeFixRatio(db, filePath),
-    computeCoverageDecline(db, repoPath, filePath),
     computeAuthorChurn(db, filePath)
   ];
 }
@@ -865,6 +700,24 @@ var MemoryAPI = class {
     });
     return this.bootstrapPromise;
   }
+  // bootstrapFromBoundary indexes only commits between fromSha and HEAD.
+  // Used by `composto index --since=YYYY-MM-DD` to bound work on huge repos.
+  // Pass fromSha=null to index the full history (same as bootstrapIfNeeded).
+  async bootstrapFromBoundary(fromSha) {
+    if (this.bootstrapPromise) return this.bootstrapPromise;
+    const head = revParseHead(this.repoPath);
+    const range = { from: fromSha, to: head };
+    this.bootstrapPromise = this.pool.runIngest({ dbPath: this.dbPath, repoPath: this.repoPath, range }).then(() => {
+      this.log.info("bootstrap_done", { through: range.to, from: range.from });
+    }).catch((err) => {
+      this.log.error("bootstrap_failed", { message: err.message });
+      this.failures.recordFailure("ingest_failure");
+      throw err;
+    }).finally(() => {
+      this.bootstrapPromise = null;
+    });
+    return this.bootstrapPromise;
+  }
   async blastradius(input) {
     const start = Date.now();
     if (this.failures.isDisabled()) {

package/dist/memory/worker.js

@@ -17,7 +17,25 @@ function openDatabase(path) {
 }
 
 // src/memory/schema.ts
-var CURRENT_VERSION = 1;
+var CURRENT_VERSION = 3;
+var V2_SQL = `
+CREATE INDEX IF NOT EXISTS idx_ft_file_commit ON file_touches(file_path, commit_sha);
+`;
+var V3_SQL = `
+CREATE TABLE IF NOT EXISTS hook_invocations (
+  id              INTEGER PRIMARY KEY AUTOINCREMENT,
+  timestamp       INTEGER NOT NULL,
+  platform        TEXT NOT NULL,
+  event           TEXT NOT NULL,
+  file_path       TEXT,
+  verdict         TEXT,
+  score           REAL,
+  confidence      REAL,
+  latency_ms      INTEGER NOT NULL,
+  cache_hit       INTEGER NOT NULL
+);
+CREATE INDEX IF NOT EXISTS idx_hi_timestamp ON hook_invocations(timestamp);
+`;
 var V1_SQL = `
 CREATE TABLE IF NOT EXISTS index_state (
   key   TEXT PRIMARY KEY,
@@ -105,7 +123,9 @@ function runMigrations(db) {
   if (current >= CURRENT_VERSION) return;
   db.exec("BEGIN");
   try {
-    db.exec(V1_SQL);
+    if (current < 1) db.exec(V1_SQL);
+    if (current < 2) db.exec(V2_SQL);
+    if (current < 3) db.exec(V3_SQL);
     db.pragma(`user_version = ${CURRENT_VERSION}`);
     db.exec("COMMIT");
   } catch (err) {
@@ -153,50 +173,40 @@ function deriveFixLinks(db) {
       (fix_commit_sha, suspected_break_sha, evidence_type, confidence, window_hours)
     VALUES (?, ?, ?, ?, ?)
   `);
-  const reverts = db.prepare(`
-    SELECT sha, reverts_sha FROM commits
-    WHERE is_revert = 1 AND reverts_sha IS NOT NULL
-  `).all();
-  for (const r of reverts) {
-    const exists = db.prepare("SELECT 1 FROM commits WHERE sha = ?").get(r.reverts_sha);
-    if (exists) insert.run(r.sha, r.reverts_sha, "revert_marker", 1, null);
-  }
-  const fixes = db.prepare(`
-    SELECT sha, timestamp FROM commits WHERE is_fix = 1
-  `).all();
-  const priorByFile = db.prepare(`
-    SELECT c.sha AS prior_sha
+  const bulkFollowup = db.prepare(`
+    INSERT OR IGNORE INTO fix_links
+      (fix_commit_sha, suspected_break_sha, evidence_type, confidence, window_hours)
+    SELECT DISTINCT
+      ft_fix.commit_sha,
+      c_prior.sha,
+      'short_followup_fix',
+      0.7,
+      ?
       FROM file_touches ft_fix
+      JOIN commits c_fix     ON c_fix.sha   = ft_fix.commit_sha   AND c_fix.is_fix = 1
       JOIN file_touches ft_prior ON ft_prior.file_path = ft_fix.file_path
-      JOIN commits c ON c.sha = ft_prior.commit_sha
-     WHERE ft_fix.commit_sha = ?
-       AND c.timestamp < ?
-       AND c.timestamp >= ?
-       AND c.sha != ?
-       AND c.is_fix = 0
-       AND c.is_revert = 0
+      JOIN commits c_prior   ON c_prior.sha = ft_prior.commit_sha
+     WHERE c_prior.timestamp <  c_fix.timestamp
+       AND c_prior.timestamp >= c_fix.timestamp - ?
+       AND c_prior.sha != c_fix.sha
+       AND c_prior.is_fix = 0
+       AND c_prior.is_revert = 0
   `);
-  for (const f of fixes) {
-    const lowerBound = f.timestamp - FOLLOWUP_WINDOW_HOURS * 3600;
-    const priors = priorByFile.all(f.sha, f.timestamp, lowerBound, f.sha);
-    const unique = new Set(priors.map((p) => p.prior_sha));
-    for (const prior of unique) {
-      insert.run(f.sha, prior, "short_followup_fix", 0.7, FOLLOWUP_WINDOW_HOURS);
-    }
-  }
-  const filesWithFixes = db.prepare(`
-    SELECT DISTINCT ft.file_path
-      FROM file_touches ft
-      JOIN commits c ON c.sha = ft.commit_sha
-     WHERE c.is_fix = 1
-  `).all();
-  const fixesOnFile = db.prepare(`
-    SELECT c.sha, c.timestamp
+  const bulkRevert = db.prepare(`
+    INSERT OR IGNORE INTO fix_links
+      (fix_commit_sha, suspected_break_sha, evidence_type, confidence, window_hours)
+    SELECT c.sha, c.reverts_sha, 'revert_marker', 1.0, NULL
       FROM commits c
-      JOIN file_touches ft ON ft.commit_sha = c.sha
-     WHERE ft.file_path = ? AND c.is_fix = 1
-     ORDER BY c.timestamp ASC
+      JOIN commits target ON target.sha = c.reverts_sha
+     WHERE c.is_revert = 1 AND c.reverts_sha IS NOT NULL
   `);
+  const allFixesByFile = db.prepare(`
+    SELECT ft.file_path, c.sha, c.timestamp
+      FROM commits c
+      JOIN file_touches ft ON ft.commit_sha = c.sha
+     WHERE c.is_fix = 1
+     ORDER BY ft.file_path, c.timestamp ASC
+  `).all();
   const priorNonFixOnFile = db.prepare(`
     SELECT c.sha
       FROM commits c
@@ -207,19 +217,29 @@ function deriveFixLinks(db) {
      ORDER BY c.timestamp DESC
      LIMIT 1
   `);
-  for (const { file_path } of filesWithFixes) {
-    const rows = fixesOnFile.all(file_path);
+  const derive = db.transaction(() => {
+    bulkRevert.run();
+    bulkFollowup.run(FOLLOWUP_WINDOW_HOURS, FOLLOWUP_WINDOW_HOURS * 3600);
     const windowSec = CHAIN_WINDOW_DAYS * 86400;
-    for (let i = 0; i + CHAIN_MIN - 1 < rows.length; i++) {
-      const windowEnd = rows[i + CHAIN_MIN - 1];
-      if (windowEnd.timestamp - rows[i].timestamp > windowSec) continue;
-      const prior = priorNonFixOnFile.get(file_path, rows[i].timestamp);
-      if (!prior) continue;
-      for (let j = i; j < rows.length && rows[j].timestamp - rows[i].timestamp <= windowSec; j++) {
-        insert.run(rows[j].sha, prior.sha, "same_region_fix_chain", 0.4, CHAIN_WINDOW_DAYS * 24);
+    let i = 0;
+    while (i < allFixesByFile.length) {
+      let j = i;
+      while (j < allFixesByFile.length && allFixesByFile[j].file_path === allFixesByFile[i].file_path) j++;
+      const rows = allFixesByFile.slice(i, j);
+      const file_path = rows[0].file_path;
+      i = j;
+      for (let k = 0; k + CHAIN_MIN - 1 < rows.length; k++) {
+        const windowEnd = rows[k + CHAIN_MIN - 1];
+        if (windowEnd.timestamp - rows[k].timestamp > windowSec) continue;
+        const prior = priorNonFixOnFile.get(file_path, rows[k].timestamp);
+        if (!prior) continue;
+        for (let m = k; m < rows.length && rows[m].timestamp - rows[k].timestamp <= windowSec; m++) {
+          insert.run(rows[m].sha, prior.sha, "same_region_fix_chain", 0.4, CHAIN_WINDOW_DAYS * 24);
+        }
       }
     }
-  }
+  });
+  derive();
 }
 
 // src/memory/calibration.ts
@@ -258,9 +278,6 @@ function validateFixRatio(db) {
   `).get().n;
   return { total, hits };
 }
-function validateCoverageDecline(_db) {
-  return { total: 0, hits: 0 };
-}
 function validateAuthorChurn(db) {
   const total = db.prepare(`SELECT COUNT(*) AS n FROM file_touches`).get().n;
   const hits = db.prepare(`SELECT COUNT(*) AS n FROM fix_links`).get().n;
@@ -270,7 +287,6 @@ var VALIDATORS = {
   revert_match: validateRevertMatch,
   hotspot: validateHotspot,
   fix_ratio: validateFixRatio,
-  coverage_decline: validateCoverageDecline,
   author_churn: validateAuthorChurn
 };
 function refreshCalibration(db, headSha) {
@@ -354,10 +370,24 @@ function parseLogOutput(output) {
   }
   return commits;
 }
+function resolveRevertsSha(raw, knownShas) {
+  if (!raw) return null;
+  if (knownShas.has(raw)) return raw;
+  if (raw.length < 40) {
+    for (const sha of knownShas) {
+      if (sha.startsWith(raw)) return sha;
+    }
+  }
+  return null;
+}
 function ingestRange(db, repoPath, range) {
   const raw = logRange(repoPath, range.from, range.to);
   const commits = parseLogOutput(raw);
   commits.sort((a, b) => a.timestamp - b.timestamp);
+  const knownShas = new Set(commits.map((c) => c.sha));
+  for (const existing of db.prepare(`SELECT sha FROM commits`).all()) {
+    knownShas.add(existing.sha);
+  }
   const insertCommit = db.prepare(`
     INSERT OR IGNORE INTO commits
       (sha, parent_sha, author, timestamp, subject, is_fix, is_revert, reverts_sha)
@@ -383,16 +413,21 @@ function ingestRange(db, repoPath, range) {
         c.subject,
         parsed.is_fix ? 1 : 0,
         parsed.is_revert ? 1 : 0,
-        parsed.reverts_sha
+        resolveRevertsSha(parsed.reverts_sha, knownShas)
       );
       for (const t of c.touches) {
         insertTouch.run(c.sha, t.file_path, t.adds, t.dels, t.change_type);
       }
     }
   });
-  const BATCH = 1e3;
-  for (let i = 0; i < commits.length; i += BATCH) {
-    tx(commits.slice(i, i + BATCH));
+  db.pragma("foreign_keys = OFF");
+  try {
+    const BATCH = 1e3;
+    for (let i = 0; i < commits.length; i += BATCH) {
+      tx(commits.slice(i, i + BATCH));
+    }
+  } finally {
+    db.pragma("foreign_keys = ON");
   }
   deriveFixLinks(db);
   if (shouldRefresh(db, range.to)) {