feat(graph): two-mode session deletion — the first destructive ledger operation

DELETE /api/chats/[id]?mode=preserve-graph|delete-nodes (mode required):
- preserve-graph: only extraction bookkeeping dies (coverage rows,
  legacy checkpoints) — graph ledgers byte-untouched
- delete-nodes: the chat's ledger traces die. Node survival = surviving
  provenance point / mapping line (notes imports carry empty
  provenance) / surviving event. The creator's aliases + provenance are
  stripped from a surviving node's create line (owner ruling
  2026-09-23: name/statement/createdAt are the shared identity);
  orphan nodes, their edges, events, mappings, positions, embedding
  vectors and cluster members die; cluster labels stay (immutable)

Gates: 404 unknown, 409 turn_in_flight / jobs_running (with jobIds),
503 extraction_winding_down after a 10s abort-and-poll; the purge is
one sync block (ledgers → jobs → chat record last). rewriteLedgers is
atomic (tmp + rename). graphRevision (max mtime over graph data files)
rides the activity feed + the response as the change stamp.

Anti-resurrection: the chat pipeline re-checks chat liveness at each
merge — a run that slips past the wind-down aborts with nothing merged
or checkpointed; its partial spend dies with the chat.

src/store/chats.ts

@@ -129,6 +129,19 @@ function renameChat(id: string, title: string): ChatRecord {
 	return record;
 }
 
+/** Delete the session record file entirely (session-deletion wave 6,
+ *  owner 2026-09-22). False when the id is unknown — the route turns that
+ *  into a 404. The record's graph traces and jobs are the route's
+ *  choreography (core/graph-deletion.ts), not the store's. */
+function deleteChat(id: string): boolean {
+	try {
+		fs.unlinkSync(chatFile(id));
+		return true;
+	} catch {
+		return false; // never existed, already deleted, or unreadable — same answer
+	}
+}
+
 /** Persist the session plan tree (plan tools call this in execute). */
 function saveTree(id: string, tree: PlanTree): void {
 	const record = getChat(id);
@@ -147,6 +160,7 @@ export const chatStore: ChatStore = {
 	saveTree,
 	saveSettings,
 	renameChat,
+	deleteChat,
 	appendTurnUsage,
 	appendExtractionUsage,
 };

src/store/graph.ts

@@ -260,6 +260,49 @@ export const graphStore: GraphStore = {
 	writeEmbeddings(ledger: EmbeddingsLedger): void {
 		writeEmbeddingsLedger(ledger);
 	},
+
+	/** THE DESTRUCTIVE SEAM (wave 6 session deletion): atomic full-content
+	 *  replacement per provided ledger — write a uniquely-named temp file
+	 *  beside the ledger, then rename over it (POSIX-atomic: a crash mid-
+	 *  write leaves the original ledger and an orphan .tmp-*, never a torn
+	 *  ledger). Empty arrays write an empty file — a purged ledger reads
+	 *  as "nothing yet", same as never-emitted. */
+	rewriteLedgers(next: {
+		nodes?: GraphNode[];
+		edges?: GraphEdge[];
+		events?: LedgerEvent[];
+		mappings?: NodeMapping[];
+		coverage?: CoverageEntry[];
+		checkpoints?: SessionCheckpoint[];
+	}): void {
+		const files = {
+			nodes: LEDGER_FILES.nodes,
+			edges: LEDGER_FILES.edges,
+			events: LEDGER_FILES.events,
+			mappings: LEDGER_FILES.mappings,
+			coverage: LEDGER_FILES.coverage,
+			checkpoints: LEDGER_FILES.sessions,
+		} as const;
+		for (const [key, records] of Object.entries(next) as [keyof typeof files, unknown[]][]) {
+			const file = files[key];
+			fs.mkdirSync(path.dirname(file), { recursive: true });
+			const tmp = `${file}.tmp-${crypto.randomUUID().slice(0, 8)}`;
+			try {
+				// JSONL: one record per line, trailing newline — a reader
+				// must see exactly what appendLine would have written.
+				const body = records.map((record) => JSON.stringify(record)).join("\n") + (records.length > 0 ? "\n" : "");
+				fs.writeFileSync(tmp, body, "utf-8");
+				fs.renameSync(tmp, file);
+			} catch (err) {
+				try {
+					fs.unlinkSync(tmp);
+				} catch {
+					/* the rename either already happened or the tmp never existed */
+				}
+				throw err;
+			}
+		}
+	},
 };
 
 /** positions.json — { positions, updatedAt }. Read-modify-write, NOT

src/store/jobs.ts

@@ -79,10 +79,28 @@ function findJobByToolCallId(chatId: string, toolCallId: string): JobRecord | nu
 	return listJobs(chatId).find((j) => j.toolCallId === toolCallId) ?? null;
 }
 
+/** Delete every job record file for a chat (session-deletion wave 6) —
+ *  running or finished, they are the chat's records and die with it.
+ *  Returns how many files were removed. The deletion route refuses while
+ *  jobs are still running, so every record here is terminal. */
+function deleteJobsForChat(chatId: string): number {
+	let removed = 0;
+	for (const job of listJobs(chatId)) {
+		try {
+			fs.unlinkSync(jobFile(job.id));
+			removed++;
+		} catch {
+			/* already gone — the count is best-effort truth */
+		}
+	}
+	return removed;
+}
+
 export const jobStore: JobStore = {
 	createJob,
 	getJob,
 	updateJob,
 	listJobs,
 	findJobByToolCallId,
+	deleteJobsForChat,
 };