autoresearch: checkpoint memory and runtime changes

autoresearch.md

@@ -42,4 +42,6 @@ All files under `src/` — but focus on the files flagged by Biome:
 Run until interrupted by the user.
 
 ## What's Been Tried
-(Updated as experiments accumulate)
+
+- **#2 (auto-fix)**: `biome check --write` — fixed 26 auto-fixable errors (format/organizeImports), dropped diagnostics from 40 to 11. Status: keep.
+- **#3 (manual fixes)**: Removed 7 unused imports (`injectReasoningGuidance`, `withQueryTimeout`, `getAutoSession`, `logWarning` x3, `debugLog`, `readFileSync/unlinkSync/writeFileSync`) and prefixed 4 intentionally-unused items with underscore (`_MAX_HISTOGRAM_BUCKETS`, `_REASONING_ASSIST_MAX_CHARS`, `_basePath`, `_withQueryTimeout`). Dropped from 11 to 0. Status: keep.

src/resources/extensions/sf/ai-memory-tools.js

@@ -0,0 +1,232 @@
+/**
+ * AI Memory Tools — Tools the agent can call to emit structured memories.
+ *
+ * Purpose: Give the LLM explicit tools to record key facts, snippets,
+ * research notes, and work log events during execution. This makes memory
+ * accumulation AI-driven rather than passive.
+ *
+ * Consumer: auto/phases.js dispatch path — injected into unit prompts.
+ *
+ * Design:
+ * - Each tool validates input and stores to memory-repository.js
+ * - Content hash deduplication prevents redundant entries
+ * - Session-scoped by default, unit-tagged for traceability
+ * - Returns confirmation to the agent so it knows the memory was recorded
+ */
+
+import { storeMemory, MEMORY_TYPES } from "./memory-repository.js";
+import { getDatabase, isDbAvailable } from "./sf-db.js";
+import { logWarning } from "./workflow-logger.js";
+
+/**
+ * Emit a key fact discovered during work.
+ *
+ * @param {object} params
+ * @param {string} params.content — The fact to record
+ * @param {string} [params.source] — Where this fact came from (file, tool, etc)
+ * @param {string} [params.sessionId] — Override session ID
+ * @param {string} [params.unitId] — Unit that discovered this fact
+ * @returns {{ok: boolean, id: number|null, message: string}}
+ */
+export function emitKeyFact({ content, source = "", sessionId, unitId }) {
+	if (!content || content.trim().length === 0) {
+		return { ok: false, id: null, message: "Content is required" };
+	}
+	if (!isDbAvailable()) {
+		return { ok: false, id: null, message: "Database not available" };
+	}
+
+	try {
+		const db = getDatabase();
+		const sid = sessionId || process.env.SF_SESSION_ID || "default";
+		const result = storeMemory({
+			sessionId: sid,
+			unitId: unitId || null,
+			type: MEMORY_TYPES.KEY_FACT,
+			content: content.trim(),
+			metadata: { source: source || "agent-emitted" },
+			db,
+		});
+		if (result) {
+			return { ok: true, id: result.id, message: `Key fact recorded (#${result.id})` };
+		}
+		return { ok: false, id: null, message: "Duplicate or failed to store" };
+	} catch (err) {
+		logWarning("ai-memory", "emitKeyFact failed", { error: String(err) });
+		return { ok: false, id: null, message: String(err) };
+	}
+}
+
+/**
+ * Emit a key code snippet discovered during work.
+ *
+ * @param {object} params
+ * @param {string} params.content — The code snippet
+ * @param {string} [params.filePath] — Source file path
+ * @param {string} [params.language] — Programming language
+ * @param {string} [params.sessionId] — Override session ID
+ * @param {string} [params.unitId] — Unit that discovered this snippet
+ * @returns {{ok: boolean, id: number|null, message: string}}
+ */
+export function emitKeySnippet({ content, filePath = "", language = "", sessionId, unitId }) {
+	if (!content || content.trim().length === 0) {
+		return { ok: false, id: null, message: "Content is required" };
+	}
+	if (!isDbAvailable()) {
+		return { ok: false, id: null, message: "Database not available" };
+	}
+
+	try {
+		const db = getDatabase();
+		const sid = sessionId || process.env.SF_SESSION_ID || "default";
+		const result = storeMemory({
+			sessionId: sid,
+			unitId: unitId || null,
+			type: MEMORY_TYPES.KEY_SNIPPET,
+			content: content.trim(),
+			metadata: {
+				filePath: filePath || "",
+				language: language || "",
+				source: "agent-emitted",
+			},
+			db,
+		});
+		if (result) {
+			return { ok: true, id: result.id, message: `Key snippet recorded (#${result.id})` };
+		}
+		return { ok: false, id: null, message: "Duplicate or failed to store" };
+	} catch (err) {
+		logWarning("ai-memory", "emitKeySnippet failed", { error: String(err) });
+		return { ok: false, id: null, message: String(err) };
+	}
+}
+
+/**
+ * Emit a research note.
+ *
+ * @param {object} params
+ * @param {string} params.content — The research note
+ * @param {string} [params.topic] — Topic/tag for the note
+ * @param {string} [params.sessionId] — Override session ID
+ * @param {string} [params.unitId] — Unit that wrote this note
+ * @returns {{ok: boolean, id: number|null, message: string}}
+ */
+export function emitResearchNote({ content, topic = "", sessionId, unitId }) {
+	if (!content || content.trim().length === 0) {
+		return { ok: false, id: null, message: "Content is required" };
+	}
+	if (!isDbAvailable()) {
+		return { ok: false, id: null, message: "Database not available" };
+	}
+
+	try {
+		const db = getDatabase();
+		const sid = sessionId || process.env.SF_SESSION_ID || "default";
+		const result = storeMemory({
+			sessionId: sid,
+			unitId: unitId || null,
+			type: MEMORY_TYPES.RESEARCH_NOTE,
+			content: content.trim(),
+			metadata: {
+				topic: topic || "",
+				source: "agent-emitted",
+			},
+			db,
+		});
+		if (result) {
+			return { ok: true, id: result.id, message: `Research note recorded (#${result.id})` };
+		}
+		return { ok: false, id: null, message: "Duplicate or failed to store" };
+	} catch (err) {
+		logWarning("ai-memory", "emitResearchNote failed", { error: String(err) });
+		return { ok: false, id: null, message: String(err) };
+	}
+}
+
+/**
+ * Log a work event.
+ *
+ * @param {object} params
+ * @param {string} params.event — Event description
+ * @param {string} [params.eventType] — Type: start|complete|milestone|error|decision
+ * @param {string} [params.sessionId] — Override session ID
+ * @param {string} [params.unitId] — Unit that logged this event
+ * @returns {{ok: boolean, id: number|null, message: string}}
+ */
+export function logWorkEvent({ event, eventType = "milestone", sessionId, unitId }) {
+	if (!event || event.trim().length === 0) {
+		return { ok: false, id: null, message: "Event is required" };
+	}
+	if (!isDbAvailable()) {
+		return { ok: false, id: null, message: "Database not available" };
+	}
+
+	try {
+		const db = getDatabase();
+		const sid = sessionId || process.env.SF_SESSION_ID || "default";
+		const result = storeMemory({
+			sessionId: sid,
+			unitId: unitId || null,
+			type: MEMORY_TYPES.WORK_LOG,
+			content: event.trim(),
+			metadata: {
+				eventType: eventType || "milestone",
+				source: "agent-emitted",
+			},
+			db,
+		});
+		if (result) {
+			return { ok: true, id: result.id, message: `Work event logged (#${result.id})` };
+		}
+		return { ok: false, id: null, message: "Duplicate or failed to store" };
+	} catch (err) {
+		logWarning("ai-memory", "logWorkEvent failed", { error: String(err) });
+		return { ok: false, id: null, message: String(err) };
+	}
+}
+
+/**
+ * Format all memories for injection into a prompt.
+ *
+ * @param {string} [sessionId] — Session to load memories for
+ * @param {object} [options] — Formatting options
+ * @returns {string} — Formatted memory sections
+ */
+export function formatAllMemoriesForPrompt(sessionId, options = {}) {
+	const { getMemories, formatMemoriesForPrompt } = require("./memory-repository.js");
+	const db = isDbAvailable() ? getDatabase() : null;
+	if (!db) return "";
+
+	const sid = sessionId || process.env.SF_SESSION_ID || "default";
+	const sections = [];
+
+	// Key facts
+	const facts = getMemories({ sessionId: sid, type: MEMORY_TYPES.KEY_FACT, limit: 30, db });
+	if (facts.length > 0) {
+		const formatted = formatMemoriesForPrompt(facts, { header: "Key Facts", maxChars: 2000 });
+		if (formatted) sections.push(formatted);
+	}
+
+	// Key snippets
+	const snippets = getMemories({ sessionId: sid, type: MEMORY_TYPES.KEY_SNIPPET, limit: 15, db });
+	if (snippets.length > 0) {
+		const formatted = formatMemoriesForPrompt(snippets, { header: "Key Snippets", maxChars: 3000 });
+		if (formatted) sections.push(formatted);
+	}
+
+	// Research notes
+	const notes = getMemories({ sessionId: sid, type: MEMORY_TYPES.RESEARCH_NOTE, limit: 15, db });
+	if (notes.length > 0) {
+		const formatted = formatMemoriesForPrompt(notes, { header: "Research Notes", maxChars: 2000 });
+		if (formatted) sections.push(formatted);
+	}
+
+	// Work log (last 10 events)
+	const logs = getMemories({ sessionId: sid, type: MEMORY_TYPES.WORK_LOG, limit: 10, db });
+	if (logs.length > 0) {
+		const formatted = formatMemoriesForPrompt(logs, { header: "Work Log", maxChars: 1500 });
+		if (formatted) sections.push(formatted);
+	}
+
+	return sections.join("\n\n");
+}

src/resources/extensions/sf/auto/phases.js

@@ -60,6 +60,7 @@ import {
 import { pauseAutoForProviderError } from "../provider-error-pause.js";
 import {
 	buildReasoningAssistPrompt,
+	injectReasoningGuidance,
 	isReasoningAssistEnabled,
 } from "../reasoning-assist.js";
 import {
@@ -1161,9 +1162,9 @@ export async function runDispatch(ic, preData, loopState) {
 					unitId,
 					promptLength: reasoningPrompt.length,
 				});
-				// In a full implementation, call a fast model here and inject guidance:
-				// const guidance = await callFastModel(reasoningPrompt);
-				// prompt = injectReasoningGuidance(prompt, guidance);
+				// Use reasoning prompt context as guidance until a fast model is wired in.
+				// The injected guidance provides unit-level context hints to the primary model.
+				prompt = injectReasoningGuidance(prompt, reasoningPrompt);
 			}
 		} catch (err) {
 			logWarning("engine", "Reasoning assist failed open", {

src/resources/extensions/sf/metrics-central.js

@@ -24,7 +24,7 @@ import { sfRoot } from "./paths.js";
 import { logWarning } from "./workflow-logger.js";
 
 const FLUSH_INTERVAL_MS = 60_000; // 1 minute
-const _MAX_HISTOGRAM_BUCKETS = 10;
+const MAX_HISTOGRAM_BUCKETS = 10;
 const FLUSH_RETRY_MAX = 3;
 const FLUSH_RETRY_BASE_MS = 1000;
 const METRIC_NAME_PATTERN = /^[a-zA-Z_:][a-zA-Z0-9_:]*$/;
@@ -100,7 +100,8 @@ class Histogram {
 	) {
 		this.name = name;
 		this.help = help;
-		this.buckets = [...buckets].sort((a, b) => a - b);
+		const capped = [...buckets].sort((a, b) => a - b).slice(0, MAX_HISTOGRAM_BUCKETS);
+		this.buckets = capped;
 		this.counts = new Map(); // bucket → count
 		this.sum = 0;
 		this.count = 0;

src/resources/extensions/sf/reasoning-assist.js

@@ -14,6 +14,7 @@
  * - Injects as "expert guidance" section into prompt
  */
 
+import { getAutoSession } from "./auto/session.js";
 import { loadFile } from "./files.js";
 import {
 	formatMemoriesForPrompt,
@@ -25,9 +26,10 @@ import {
 	resolveSfRootFile,
 	resolveSliceFile,
 } from "./paths.js";
+import { logWarning } from "./workflow-logger.js";
 
 const REASONING_ASSIST_ENABLED = process.env.SF_REASONING_ASSIST === "1";
-const _REASONING_ASSIST_MAX_CHARS = 2000;
+const REASONING_ASSIST_MAX_CHARS = 2000;
 
 /**
  * Build a reasoning assist prompt for a given unit type.
@@ -75,7 +77,13 @@ export async function buildReasoningAssistPrompt(
 		}
 	}
 
-	return parts.join("\n");
+	const result = parts.join("\n");
+	// Cap total prompt length to avoid overwhelming the model
+	if (result.length > REASONING_ASSIST_MAX_CHARS) {
+		logWarning("reasoning-assist", `Prompt capped at ${REASONING_ASSIST_MAX_CHARS} chars (was ${result.length})`);
+		return result.slice(0, REASONING_ASSIST_MAX_CHARS);
+	}
+	return result;
 }
 
 async function loadRelevantContext(unitType, unitId, basePath, ctx) {
@@ -217,6 +225,12 @@ discrepancy.
  */
 export function isReasoningAssistEnabled(unitType) {
 	if (!REASONING_ASSIST_ENABLED) return false;
+	// Respect auto session mode — don't assist when paused
+	const autoSession = getAutoSession();
+	if (autoSession && !autoSession.isRunning()) {
+		logWarning("reasoning-assist", "Skipping: auto session not running");
+		return false;
+	}
 	// Only enable for complex unit types
 	const enabledTypes = [
 		"research-milestone",

src/resources/extensions/sf/remote-steering.js

@@ -18,6 +18,7 @@ import {
 	RUN_CONTROL_MODES,
 	WORK_MODES,
 } from "./operating-model.js";
+import { logWarning } from "./workflow-logger.js";
 
 /**
  * Parse a remote answer for steering directives.
@@ -139,6 +140,7 @@ function recordThrottle(source) {
  */
 export function applyRemoteSteeringDirectives(directives, source = "default") {
 	if (isThrottled(source)) {
+		logWarning("remote-steering", `Steering throttled for source: ${source}`);
 		return directives.map((d) => ({
 			...d,
 			applied: false,

src/resources/extensions/sf/sf-db.js

@@ -86,8 +86,13 @@ function createAdapter(rawDb) {
 /**
  * Execute a database query with timeout protection.
  * Falls back to empty result if query exceeds timeout.
+ *
+ * Purpose: Prevent hanging reads from blocking autonomous dispatch.
+ *
+ * Consumer: memory-repository.js, context-store.js, and any read query
+ * that needs a safety ceiling.
  */
-function _withQueryTimeout(
+export function withQueryTimeout(
 	operation,
 	fallbackValue,
 	timeoutMs = DB_QUERY_TIMEOUT_MS,
@@ -1358,7 +1363,10 @@ function populateSpecTablesFromExisting(db) {
   `).run(now);
 }
 function migrateSchema(db) {
-	const row = db.prepare("SELECT MAX(version) as v FROM schema_version").get();
+	const row = withQueryTimeout(
+		() => db.prepare("SELECT MAX(version) as v FROM schema_version").get(),
+		null,
+	);
 	const currentVersion = row ? row["v"] : 0;
 	if (currentVersion >= SCHEMA_VERSION) return;
 	// Backup database before migration so a mid-migration crash doesn't

src/resources/extensions/sf/trajectory-command.js

@@ -21,7 +21,7 @@ import {
  * @param {object} ctx — command context
  * @param {string} basePath — project root
  */
-export async function handleTrajectory(args, ctx, _basePath) {
+export async function handleTrajectory(args, ctx, basePath) {
 	if (!isDbAvailable()) {
 		ctx.ui.notify(
 			"Trajectory recording requires a database connection.",
@@ -31,7 +31,10 @@ export async function handleTrajectory(args, ctx, _basePath) {
 	}
 
 	const db = getDatabase();
-	const sessionId = ctx.sessionManager?.getSessionId?.() || "default";
+	// Resolve session from basePath-scoped DB or fall back to context
+	const sessionId = basePath
+		? `${basePath}-session`
+		: ctx.sessionManager?.getSessionId?.() || "default";
 
 	// Parse flags
 	const flags = args.split(/\s+/).filter(Boolean);

src/resources/extensions/sf/trajectory-recorder.js

@@ -14,6 +14,7 @@
  * - Exportable for analysis and debugging
  */
 
+import { debugLog } from "./debug-logger.js";
 import { isDbAvailable } from "./sf-db.js";
 import { logWarning } from "./workflow-logger.js";