fix(agent-core-v2): harden file-history checkpoints per review

Delta-encode the durable checkpoint events (unchanged entries fold back
in from the previous checkpoint) so wire growth stops scaling with turns
times tracked files. Make the over-budget diff approximation order-aware
(greedy common subsequence) so reordered large files no longer report
zero-change stats. Store and read path-keyed entries prototype-free so
filenames like __proto__ record correctly.

Author: user

packages/agent-core-v2/src/features/fileHistory/fileHistoryOps.ts

@@ -67,21 +67,35 @@ export function checkpointPhaseOf(record: {
   return record.phase ?? 'start';
 }
 
+function cloneEntries(
+  entries: Readonly<Record<string, FileBackupEntry>>,
+): Record<string, FileBackupEntry> {
+  const clone: Record<string, FileBackupEntry> = Object.create(null) as Record<
+    string,
+    FileBackupEntry
+  >;
+  for (const [path, entry] of Object.entries(entries)) clone[path] = entry;
+  return clone;
+}
+
 export const fileHistoryKey = defineState(
   'fileHistory',
   (): FileHistoryState => ({ checkpoints: [], tracked: [] }),
 )
   .replayable({ schema: z.custom<FileHistoryState>() })
   .on(FileHistoryCheckpointed, (s, e) => {
     const phase = checkpointPhaseOf(e);
+    const base = s.checkpoints.at(-1)?.entries;
+    const merged = cloneEntries(base ?? {});
+    for (const [path, entry] of Object.entries(e.entries)) merged[path] = { ...entry };
     const existing = s.checkpoints.find(
       (c) => c.turnId === e.turnId && checkpointPhaseOf(c) === phase,
     );
     if (existing !== undefined) {
-      existing.entries = { ...e.entries };
+      existing.entries = merged;
       return;
     }
-    s.checkpoints.push({ turnId: e.turnId, phase, entries: { ...e.entries } });
+    s.checkpoints.push({ turnId: e.turnId, phase, entries: merged });
     if (s.checkpoints.length > FILE_HISTORY_CHECKPOINT_CAP) {
       s.checkpoints.splice(0, s.checkpoints.length - FILE_HISTORY_CHECKPOINT_CAP);
     }
@@ -95,7 +109,7 @@ export const fileHistoryKey = defineState(
       s.checkpoints.push({ turnId: e.turnId, phase: 'start', entries: {} });
       checkpoint = s.checkpoints.at(-1);
     }
-    if (checkpoint !== undefined && checkpoint.entries[e.path] === undefined) {
+    if (checkpoint !== undefined && !Object.hasOwn(checkpoint.entries, e.path)) {
       checkpoint.entries[e.path] = { ...e.entry };
     }
   });

packages/agent-core-v2/src/features/fileHistory/fileHistoryService.ts

@@ -179,25 +179,21 @@ export class AgentFileHistoryService extends Service implements IAgentFileHistor
       return;
     }
 
-    const entries: Record<string, FileBackupEntry> = {};
+    const entries: Record<string, FileBackupEntry> = Object.create(null) as Record<
+      string,
+      FileBackupEntry
+    >;
     for (const pathKey of state.tracked) {
       const latest = latestEntry(state.checkpoints, pathKey);
       const nextVersion = maxVersion(state.checkpoints, pathKey) + 1;
       const current = await this.readCurrent(pathKey);
-      if (current === 'unreadable') {
-        if (latest !== undefined) entries[pathKey] = latest;
-        continue;
-      }
+      if (current === 'unreadable') continue;
       if (current === 'missing') {
-        entries[pathKey] =
-          latest?.key === null ? latest : { key: null, version: nextVersion };
+        if (latest?.key !== null) entries[pathKey] = { key: null, version: nextVersion };
         continue;
       }
       const contentHash = sha256(current);
-      if (latest !== undefined && latest.contentHash === contentHash) {
-        entries[pathKey] = latest;
-        continue;
-      }
+      if (latest !== undefined && latest.contentHash === contentHash) continue;
       entries[pathKey] = await this.backup(pathKey, nextVersion, current, contentHash);
     }
 
@@ -292,8 +288,8 @@ function entryAt(
   path: string,
 ): FileBackupEntry | undefined {
   for (let i = index; i >= 0; i -= 1) {
-    const entry = checkpoints[i]!.entries[path];
-    if (entry !== undefined) return entry;
+    const record = checkpoints[i]!.entries;
+    if (Object.hasOwn(record, path)) return record[path];
   }
   return undefined;
 }
@@ -311,7 +307,7 @@ function maxVersion(
 ): number {
   let max = 0;
   for (const checkpoint of checkpoints) {
-    const entry = checkpoint.entries[path];
+    const entry = Object.hasOwn(checkpoint.entries, path) ? checkpoint.entries[path] : undefined;
     if (entry !== undefined && entry.version > max) max = entry.version;
   }
   return max;
@@ -430,14 +426,23 @@ const LCS_CELL_BUDGET = 4_000_000;
 function lcsLength(a: readonly string[], b: readonly string[]): number {
   if (a.length === 0 || b.length === 0) return 0;
   if (a.length * b.length > LCS_CELL_BUDGET) {
-    const remaining = new Map<string, number>();
-    for (const line of b) remaining.set(line, (remaining.get(line) ?? 0) + 1);
     let common = 0;
+    const positions = new Map<string, number[]>();
+    for (let j = b.length - 1; j >= 0; j -= 1) {
+      const line = b[j]!;
+      const list = positions.get(line);
+      if (list === undefined) positions.set(line, [j]);
+      else list.push(j);
+    }
+    let cursor = 0;
     for (const line of a) {
-      const left = remaining.get(line) ?? 0;
-      if (left > 0) {
+      const list = positions.get(line);
+      if (list === undefined) continue;
+      while (list.length > 0 && list[list.length - 1]! < cursor) list.pop();
+      const match = list.pop();
+      if (match !== undefined) {
         common += 1;
-        remaining.set(line, left - 1);
+        cursor = match + 1;
       }
     }
     return common;

packages/agent-core-v2/test/features/fileHistory/fileHistory.test.ts

@@ -324,6 +324,15 @@ describe('AgentFileHistoryService', () => {
     expect(diff.deletions).toBe(901);
   });
 
+  it('keeps over-budget diff approximations order-aware on reordered files', () => {
+    const lines = Array.from({ length: 3000 }, (_, i) => `line-${String(i)}`);
+    const before = [...lines, 'tail-old'].join('\n');
+    const after = ['head-new', ...lines.toReversed()].join('\n');
+    const diff = countLineDiff(before, after);
+    expect(diff.additions).toBeGreaterThan(2000);
+    expect(diff.deletions).toBeGreaterThan(2000);
+  });
+
   it('stays inactive on subagents', async () => {
     const service = createService('sub-1');
     setFile('/ws/a.txt', 'content\n');