pi-continuous-learning 0.4.0 → 0.5.0

package/README.md

@@ -95,6 +95,32 @@ The script:
 - **Global timeout:** The process exits after 5 minutes regardless of progress.
 - **Stale lock detection:** If a previous run crashed, the lockfile is automatically cleaned up after 10 minutes or if the owning process is no longer alive.
 
+### Logging
+
+The analyzer writes structured JSON logs to `~/.pi/continuous-learning/analyzer.log` (configurable via `log_path` in config). Each run logs:
+
+- **Run timing** - total duration and per-project duration
+- **Token usage** - input, output, cache read/write, total
+- **Cost** - USD cost per project and total
+- **Instinct changes** - counts of created, updated, and deleted instincts
+- **Skip reasons** - why projects were skipped (no new observations, below threshold, etc.)
+- **Errors** - full error details with stack traces
+
+Each log line is a JSON object, making it easy to parse with `jq`:
+
+```bash
+# View recent run summaries
+cat ~/.pi/continuous-learning/analyzer.log | jq 'select(.event == "run_complete")'
+
+# Check total cost over time
+cat ~/.pi/continuous-learning/analyzer.log | jq 'select(.event == "run_complete") | .total_cost_usd'
+
+# See which projects were processed
+cat ~/.pi/continuous-learning/analyzer.log | jq 'select(.event == "project_complete") | {project: .project_name, duration_s: (.duration_ms/1000), cost: .cost_usd}'
+```
+
+The log file auto-rotates at 10 MB (old content moved to `analyzer.log.old`). When the log file is not writable, output falls back to stderr.
+
 ### Setting up a schedule (macOS)
 
 The recommended way to run the analyzer on a recurring schedule on macOS is with `launchd`, which persists across reboots and handles log rotation.
@@ -124,9 +150,9 @@ cat > ~/Library/LaunchAgents/com.pi-continuous-learning.analyze.plist << EOF
     <key>StartInterval</key>
     <integer>300</integer>
     <key>StandardOutPath</key>
-    <string>/tmp/pi-cl-analyze.log</string>
+    <string>/tmp/pi-cl-analyze-stdout.log</string>
     <key>StandardErrorPath</key>
-    <string>/tmp/pi-cl-analyze.log</string>
+    <string>/tmp/pi-cl-analyze-stderr.log</string>
     <key>EnvironmentVariables</key>
     <dict>
         <key>PATH</key>
@@ -153,8 +179,11 @@ The analyzer will now run every 5 minutes (300 seconds) in the background, start
 # Check if the job is loaded
 launchctl list | grep pi-continuous-learning
 
-# View recent output
-tail -20 /tmp/pi-cl-analyze.log
+# View recent log entries (structured JSON)
+tail -5 ~/.pi/continuous-learning/analyzer.log | jq .
+
+# View stderr output (fallback only)
+tail -20 /tmp/pi-cl-analyze-stderr.log
 ```
 
 #### Disabling the schedule
@@ -186,7 +215,7 @@ Use cron:
 crontab -e
 
 # Add this line (runs every 5 minutes):
-*/5 * * * * pi-cl-analyze >> /tmp/pi-cl-analyze.log 2>&1
+*/5 * * * * pi-cl-analyze 2>> /tmp/pi-cl-analyze-stderr.log
 ```
 
 To disable, remove the line from `crontab -e`.
@@ -273,6 +302,7 @@ Only include the fields you want to change — missing fields use the defaults a
 | `max_injection_chars` | 4000 | Character budget for the injection block (~1000 tokens) |
 | `model` | `claude-haiku-4-5` | Model for the background analyzer (lightweight models recommended to minimize cost) |
 | `timeout_seconds` | 120 | Per-project timeout for the analyzer LLM session |
+| `log_path` | `~/.pi/continuous-learning/analyzer.log` | Path to the analyzer log file |
 
 ## Storage
 

package/dist/cli/analyze-logger.d.ts

@@ -0,0 +1,63 @@
+/**
+ * Structured logging for the background analyzer CLI.
+ * Writes to a configurable log file (default: ~/.pi/continuous-learning/analyzer.log).
+ * Each line is a JSON object for easy parsing and grep-ability.
+ *
+ * Log levels: info, warn, error
+ * Never throws - all I/O failures fall back to stderr.
+ */
+export interface ProjectRunStats {
+    readonly project_id: string;
+    readonly project_name: string;
+    readonly duration_ms: number;
+    readonly observations_processed: number;
+    readonly observations_total: number;
+    readonly instincts_created: number;
+    readonly instincts_updated: number;
+    readonly instincts_deleted: number;
+    readonly tokens_input: number;
+    readonly tokens_output: number;
+    readonly tokens_cache_read: number;
+    readonly tokens_cache_write: number;
+    readonly tokens_total: number;
+    readonly cost_usd: number;
+    readonly model: string;
+    readonly skipped_reason?: string;
+}
+export interface RunSummary {
+    readonly total_duration_ms: number;
+    readonly projects_processed: number;
+    readonly projects_skipped: number;
+    readonly projects_errored: number;
+    readonly projects_total: number;
+    readonly total_tokens: number;
+    readonly total_cost_usd: number;
+    readonly total_instincts_created: number;
+    readonly total_instincts_updated: number;
+    readonly total_instincts_deleted: number;
+    readonly project_stats: readonly ProjectRunStats[];
+}
+export declare class AnalyzeLogger {
+    private readonly logPath;
+    constructor(logPath?: string);
+    getLogPath(): string;
+    info(message: string, data?: Record<string, unknown>): void;
+    warn(message: string, data?: Record<string, unknown>): void;
+    error(message: string, error?: unknown, data?: Record<string, unknown>): void;
+    /** Log the start of a full analyzer run */
+    runStart(projectCount: number): void;
+    /** Log that a project was skipped (with reason) */
+    projectSkipped(projectId: string, projectName: string, reason: string): void;
+    /** Log the start of a project analysis */
+    projectStart(projectId: string, projectName: string, newObservations: number, totalObservations: number): void;
+    /** Log per-project results after analysis completes */
+    projectComplete(stats: ProjectRunStats): void;
+    /** Log a project that errored during analysis */
+    projectError(projectId: string, projectName: string, error: unknown): void;
+    /** Log the full run summary */
+    runComplete(summary: RunSummary): void;
+    private ensureLogDir;
+    private write;
+    private rotateIfNeeded;
+}
+//# sourceMappingURL=analyze-logger.d.ts.map

package/dist/cli/analyze-logger.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/analyze-logger.js

@@ -0,0 +1,140 @@
+/**
+ * Structured logging for the background analyzer CLI.
+ * Writes to a configurable log file (default: ~/.pi/continuous-learning/analyzer.log).
+ * Each line is a JSON object for easy parsing and grep-ability.
+ *
+ * Log levels: info, warn, error
+ * Never throws - all I/O failures fall back to stderr.
+ */
+import { appendFileSync, mkdirSync, renameSync, statSync } from "node:fs";
+import { dirname } from "node:path";
+import { join } from "node:path";
+import { getBaseDir } from "../storage.js";
+// ---------------------------------------------------------------------------
+// Constants
+// ---------------------------------------------------------------------------
+const DEFAULT_LOG_FILENAME = "analyzer.log";
+const MAX_LOG_SIZE_BYTES = 10 * 1024 * 1024; // 10 MB - rotate beyond this
+// ---------------------------------------------------------------------------
+// Logger
+// ---------------------------------------------------------------------------
+export class AnalyzeLogger {
+    logPath;
+    constructor(logPath) {
+        this.logPath = logPath ?? join(getBaseDir(), DEFAULT_LOG_FILENAME);
+        this.ensureLogDir();
+    }
+    getLogPath() {
+        return this.logPath;
+    }
+    info(message, data) {
+        this.write("info", message, data);
+    }
+    warn(message, data) {
+        this.write("warn", message, data);
+    }
+    error(message, error, data) {
+        const errorData = { ...data };
+        if (error instanceof Error) {
+            errorData.error_message = error.message;
+            errorData.error_stack = error.stack;
+        }
+        else if (error !== undefined) {
+            errorData.error_message = String(error);
+        }
+        this.write("error", message, errorData);
+    }
+    /** Log the start of a full analyzer run */
+    runStart(projectCount) {
+        this.info("Analyzer run started", {
+            event: "run_start",
+            project_count: projectCount,
+            pid: process.pid,
+        });
+    }
+    /** Log that a project was skipped (with reason) */
+    projectSkipped(projectId, projectName, reason) {
+        this.info(`Skipped ${projectName}`, {
+            event: "project_skipped",
+            project_id: projectId,
+            project_name: projectName,
+            reason,
+        });
+    }
+    /** Log the start of a project analysis */
+    projectStart(projectId, projectName, newObservations, totalObservations) {
+        this.info(`Processing ${projectName}`, {
+            event: "project_start",
+            project_id: projectId,
+            project_name: projectName,
+            new_observations: newObservations,
+            total_observations: totalObservations,
+        });
+    }
+    /** Log per-project results after analysis completes */
+    projectComplete(stats) {
+        const durationSec = (stats.duration_ms / 1000).toFixed(1);
+        const costFormatted = stats.cost_usd.toFixed(4);
+        this.info(`Completed ${stats.project_name} in ${durationSec}s - ` +
+            `tokens: ${stats.tokens_total}, cost: $${costFormatted}, ` +
+            `instincts: +${stats.instincts_created} ~${stats.instincts_updated} -${stats.instincts_deleted}`, { event: "project_complete", ...stats });
+    }
+    /** Log a project that errored during analysis */
+    projectError(projectId, projectName, error) {
+        this.error(`Error processing ${projectName}`, error, {
+            event: "project_error",
+            project_id: projectId,
+            project_name: projectName,
+        });
+    }
+    /** Log the full run summary */
+    runComplete(summary) {
+        const durationSec = (summary.total_duration_ms / 1000).toFixed(1);
+        const costFormatted = summary.total_cost_usd.toFixed(4);
+        this.info(`Run complete in ${durationSec}s - ` +
+            `${summary.projects_processed}/${summary.projects_total} projects processed, ` +
+            `${summary.projects_skipped} skipped, ${summary.projects_errored} errored - ` +
+            `tokens: ${summary.total_tokens}, cost: $${costFormatted}, ` +
+            `instincts: +${summary.total_instincts_created} ~${summary.total_instincts_updated} -${summary.total_instincts_deleted}`, { event: "run_complete", ...summary });
+    }
+    // -------------------------------------------------------------------------
+    // Internal
+    // -------------------------------------------------------------------------
+    ensureLogDir() {
+        try {
+            mkdirSync(dirname(this.logPath), { recursive: true });
+        }
+        catch {
+            // Best effort
+        }
+    }
+    write(level, message, data) {
+        const entry = {
+            timestamp: new Date().toISOString(),
+            level,
+            message,
+            ...data,
+        };
+        const line = JSON.stringify(entry) + "\n";
+        try {
+            this.rotateIfNeeded();
+            appendFileSync(this.logPath, line, "utf-8");
+        }
+        catch {
+            // Fall back to stderr - never lose log entries entirely
+            process.stderr.write(`[analyze] ${line}`);
+        }
+    }
+    rotateIfNeeded() {
+        try {
+            const stat = statSync(this.logPath);
+            if (stat.size > MAX_LOG_SIZE_BYTES) {
+                renameSync(this.logPath, this.logPath + ".old");
+            }
+        }
+        catch {
+            // File doesn't exist yet or stat failed - fine
+        }
+    }
+}
+//# sourceMappingURL=analyze-logger.js.map

package/dist/cli/analyze-logger.js.map

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package/dist/cli/analyze.js

@@ -12,11 +12,12 @@ import { buildAnalyzerSystemPrompt } from "./analyze-prompt.js";
 import { createInstinctListTool, createInstinctReadTool, createInstinctWriteTool, createInstinctDeleteTool, } from "../instinct-tools.js";
 import { readAgentsMd } from "../agents-md.js";
 import { homedir } from "node:os";
+import { AnalyzeLogger } from "./analyze-logger.js";
 // ---------------------------------------------------------------------------
-// Lockfile guard — ensures only one instance runs at a time
+// Lockfile guard - ensures only one instance runs at a time
 // ---------------------------------------------------------------------------
 const LOCKFILE_NAME = "analyze.lock";
-const LOCK_STALE_MS = 10 * 60 * 1000; // 10 minutes — stale lock threshold
+const LOCK_STALE_MS = 10 * 60 * 1000; // 10 minutes - stale lock threshold
 function getLockfilePath(baseDir) {
     return join(baseDir, LOCKFILE_NAME);
 }
@@ -33,14 +34,14 @@ function acquireLock(baseDir) {
                 if (age < LOCK_STALE_MS) {
                     return false; // Process alive and lock is fresh
                 }
-                // Process alive but lock is stale — treat as abandoned
+                // Process alive but lock is stale - treat as abandoned
             }
             catch {
-                // Process is dead — lock is orphaned, safe to take over
+                // Process is dead - lock is orphaned, safe to take over
             }
         }
         catch {
-            // Malformed lockfile — remove and proceed
+            // Malformed lockfile - remove and proceed
         }
     }
     writeFileSync(lockPath, JSON.stringify({ pid: process.pid, started_at: new Date().toISOString() }), "utf-8");
@@ -53,19 +54,55 @@ function releaseLock(baseDir) {
             unlinkSync(lockPath);
     }
     catch {
-        // Best effort — don't crash on cleanup
+        // Best effort - don't crash on cleanup
     }
 }
 // ---------------------------------------------------------------------------
 // Global timeout
 // ---------------------------------------------------------------------------
 const DEFAULT_TIMEOUT_MS = 5 * 60 * 1000; // 5 minutes total
-function startGlobalTimeout(timeoutMs) {
+function startGlobalTimeout(timeoutMs, logger) {
     setTimeout(() => {
-        console.error("[analyze] Global timeout reached. Exiting.");
+        logger.error("Global timeout reached, forcing exit");
         process.exit(2);
     }, timeoutMs).unref();
 }
+/**
+ * Wraps instinct tools to count create/update/delete operations.
+ * Returns new tool instances that increment the provided counts.
+ */
+function wrapInstinctToolsWithTracking(projectId, projectName, baseDir, counts) {
+    const writeTool = createInstinctWriteTool(projectId, projectName, baseDir);
+    const deleteTool = createInstinctDeleteTool(projectId, baseDir);
+    const trackedWrite = {
+        ...writeTool,
+        async execute(toolCallId, params, signal, onUpdate, ctx) {
+            const result = await writeTool.execute(toolCallId, params, signal, onUpdate, ctx);
+            const details = result.details;
+            if (details?.action === "created") {
+                counts.created++;
+            }
+            else {
+                counts.updated++;
+            }
+            return result;
+        },
+    };
+    const trackedDelete = {
+        ...deleteTool,
+        async execute(toolCallId, params, signal, onUpdate, ctx) {
+            const result = await deleteTool.execute(toolCallId, params, signal, onUpdate, ctx);
+            counts.deleted++;
+            return result;
+        },
+    };
+    return {
+        listTool: createInstinctListTool(projectId, baseDir),
+        readTool: createInstinctReadTool(projectId, baseDir),
+        writeTool: trackedWrite,
+        deleteTool: trackedDelete,
+    };
+}
 function loadProjectsRegistry(baseDir) {
     const path = getProjectsRegistryPath(baseDir);
     if (!existsSync(path))
@@ -104,19 +141,23 @@ function hasNewObservations(projectId, meta, baseDir) {
     }
     return true;
 }
-async function analyzeProject(project, config, baseDir) {
+async function analyzeProject(project, config, baseDir, logger) {
     const meta = loadProjectMeta(project.id, baseDir);
-    if (!hasNewObservations(project.id, meta, baseDir))
-        return false;
+    if (!hasNewObservations(project.id, meta, baseDir)) {
+        return { ran: false, skippedReason: "no new observations" };
+    }
     const obsPath = getObservationsPath(project.id, baseDir);
     const sinceLineCount = meta.last_observation_line_count ?? 0;
     const { lines: newObsLines, totalLineCount } = tailObservationsSince(obsPath, sinceLineCount);
-    if (newObsLines.length === 0)
-        return false;
+    if (newObsLines.length === 0) {
+        return { ran: false, skippedReason: "no new observation lines" };
+    }
     const obsCount = countObservations(project.id, baseDir);
-    if (obsCount < config.min_observations_to_analyze)
-        return false;
-    console.log(`[analyze] Processing ${project.name} (${project.id}): ${newObsLines.length} new observations (${obsCount} total)`);
+    if (obsCount < config.min_observations_to_analyze) {
+        return { ran: false, skippedReason: `below threshold (${obsCount}/${config.min_observations_to_analyze})` };
+    }
+    const startTime = Date.now();
+    logger.projectStart(project.id, project.name, newObsLines.length, obsCount);
     runDecayPass(project.id, baseDir);
     const instinctsDir = join(getProjectDir(project.id, baseDir), "instincts", "personal");
     const agentsMdProject = readAgentsMd(join(project.root, "AGENTS.md"));
@@ -131,7 +172,7 @@ async function analyzeProject(project, config, baseDir) {
         }));
     }
     catch {
-        // Skills loading is best-effort — continue without them
+        // Skills loading is best-effort - continue without them
     }
     const userPrompt = buildAnalyzerUserPrompt(obsPath, instinctsDir, project, {
         agentsMdProject,
@@ -143,11 +184,14 @@ async function analyzeProject(project, config, baseDir) {
     const modelRegistry = new ModelRegistry(authStorage);
     const modelId = (config.model || DEFAULT_CONFIG.model);
     const model = getModel("anthropic", modelId);
+    // Track instinct operations
+    const instinctCounts = { created: 0, updated: 0, deleted: 0 };
+    const trackedTools = wrapInstinctToolsWithTracking(project.id, project.name, baseDir, instinctCounts);
     const customTools = [
-        createInstinctListTool(project.id, baseDir),
-        createInstinctReadTool(project.id, baseDir),
-        createInstinctWriteTool(project.id, project.name, baseDir),
-        createInstinctDeleteTool(project.id, baseDir),
+        trackedTools.listTool,
+        trackedTools.readTool,
+        trackedTools.writeTool,
+        trackedTools.deleteTool,
     ];
     const loader = new DefaultResourceLoader({
         systemPromptOverride: () => buildAnalyzerSystemPrompt(),
@@ -167,40 +211,88 @@ async function analyzeProject(project, config, baseDir) {
     finally {
         session.dispose();
     }
+    // Collect stats after session completes
+    const sessionStats = session.getSessionStats();
+    const durationMs = Date.now() - startTime;
+    const stats = {
+        project_id: project.id,
+        project_name: project.name,
+        duration_ms: durationMs,
+        observations_processed: newObsLines.length,
+        observations_total: obsCount,
+        instincts_created: instinctCounts.created,
+        instincts_updated: instinctCounts.updated,
+        instincts_deleted: instinctCounts.deleted,
+        tokens_input: sessionStats.tokens.input,
+        tokens_output: sessionStats.tokens.output,
+        tokens_cache_read: sessionStats.tokens.cacheRead,
+        tokens_cache_write: sessionStats.tokens.cacheWrite,
+        tokens_total: sessionStats.tokens.total,
+        cost_usd: sessionStats.cost,
+        model: modelId,
+    };
+    logger.projectComplete(stats);
     saveProjectMeta(project.id, { ...meta, last_analyzed_at: new Date().toISOString(), last_observation_line_count: totalLineCount }, baseDir);
-    console.log(`[analyze] Completed ${project.name}`);
-    return true;
+    return { ran: true, stats };
 }
 // ---------------------------------------------------------------------------
 // Main
 // ---------------------------------------------------------------------------
 async function main() {
     const baseDir = getBaseDir();
+    const config = loadConfig();
+    const logger = new AnalyzeLogger(config.log_path);
     if (!acquireLock(baseDir)) {
-        console.log("[analyze] Another instance is already running. Exiting.");
+        logger.info("Another instance is already running, exiting");
         process.exit(0);
     }
-    startGlobalTimeout(DEFAULT_TIMEOUT_MS);
+    startGlobalTimeout(DEFAULT_TIMEOUT_MS, logger);
+    const runStart = Date.now();
     try {
-        const config = loadConfig();
         const registry = loadProjectsRegistry(baseDir);
         const projects = Object.values(registry);
         if (projects.length === 0) {
-            console.log("[analyze] No projects registered. Use pi with the continuous-learning extension first.");
+            logger.info("No projects registered");
             return;
         }
+        logger.runStart(projects.length);
         let processed = 0;
+        let skipped = 0;
+        let errored = 0;
+        const allProjectStats = [];
         for (const project of projects) {
             try {
-                const didRun = await analyzeProject(project, config, baseDir);
-                if (didRun)
+                const result = await analyzeProject(project, config, baseDir, logger);
+                if (result.ran && result.stats) {
                     processed++;
+                    allProjectStats.push(result.stats);
+                }
+                else {
+                    skipped++;
+                    if (result.skippedReason) {
+                        logger.projectSkipped(project.id, project.name, result.skippedReason);
+                    }
+                }
             }
             catch (err) {
-                console.error(`[analyze] Error processing ${project.name}: ${String(err)}`);
+                errored++;
+                logger.projectError(project.id, project.name, err);
             }
         }
-        console.log(`[analyze] Done. Processed ${processed}/${projects.length} project(s).`);
+        const summary = {
+            total_duration_ms: Date.now() - runStart,
+            projects_processed: processed,
+            projects_skipped: skipped,
+            projects_errored: errored,
+            projects_total: projects.length,
+            total_tokens: allProjectStats.reduce((sum, s) => sum + s.tokens_total, 0),
+            total_cost_usd: allProjectStats.reduce((sum, s) => sum + s.cost_usd, 0),
+            total_instincts_created: allProjectStats.reduce((sum, s) => sum + s.instincts_created, 0),
+            total_instincts_updated: allProjectStats.reduce((sum, s) => sum + s.instincts_updated, 0),
+            total_instincts_deleted: allProjectStats.reduce((sum, s) => sum + s.instincts_deleted, 0),
+            project_stats: allProjectStats,
+        };
+        logger.runComplete(summary);
     }
     finally {
         releaseLock(baseDir);
@@ -208,7 +300,9 @@ async function main() {
 }
 main().catch((err) => {
     releaseLock(getBaseDir());
-    console.error(`[analyze] Fatal error: ${String(err)}`);
+    // Last-resort logging - config may not have loaded
+    const logger = new AnalyzeLogger();
+    logger.error("Fatal error", err);
     process.exit(1);
 });
 //# sourceMappingURL=analyze.js.map

package/dist/cli/analyze.js.map

@@ -1 +1 @@
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package/dist/config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAOH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,YAAY,CAAC;AAMzC;;;GAGG;AACH,eAAO,MAAM,aAAa,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAWhD,CAAC;AAEF,eAAO,MAAM,WAAW,QAKvB,CAAC;AAEF,eAAO,MAAM,cAAc,EAAE,MAW5B,CAAC;AA4BF;;;;GAIG;AACH,wBAAgB,UAAU,IAAI,MAAM,CA2BnC"}

package/dist/config.js

@@ -53,6 +53,7 @@ const PartialConfigSchema = Type.Partial(Type.Object({
     active_hours_start: Type.Number(),
     active_hours_end: Type.Number(),
     max_idle_seconds: Type.Number(),
+    log_path: Type.String(),
 }));
 // ---------------------------------------------------------------------------
 // loadConfig

package/dist/config.js.map

@@ -1 +1 @@
-{"version":3,"file":"config.js","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,IAAI,EAAe,MAAM,mBAAmB,CAAC;AACtD,OAAO,EAAE,KAAK,EAAE,MAAM,yBAAyB,CAAC;AAGhD,8EAA8E;AAC9E,YAAY;AACZ,8EAA8E;AAE9E;;;GAGG;AACH,MAAM,CAAC,MAAM,aAAa,GAA2B;IACnD,GAAG,EAAE,mCAAmC;IACxC,OAAO,EAAE,kCAAkC;IAC3C,SAAS,EAAE,8BAA8B;IACzC,QAAQ,EAAE,qCAAqC;IAC/C,UAAU,EAAE,qCAAqC;IACjD,GAAG,EAAE,iBAAiB;IACtB,MAAM,EAAE,kCAAkC;IAC1C,QAAQ,EAAE,iDAAiD;IAC3D,WAAW,EAAE,0BAA0B;IACvC,aAAa,EAAE,qCAAqC;CACrD,CAAC;AAEF,MAAM,CAAC,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAClC,EAAE,CAAC,OAAO,EAAE,EACZ,KAAK,EACL,qBAAqB,EACrB,aAAa,CACd,CAAC;AAEF,MAAM,CAAC,MAAM,cAAc,GAAW;IACpC,oBAAoB,EAAE,CAAC;IACvB,2BAA2B,EAAE,EAAE;IAC/B,cAAc,EAAE,GAAG;IACnB,aAAa,EAAE,EAAE;IACjB,mBAAmB,EAAE,IAAI;IACzB,KAAK,EAAE,kBAAkB;IACzB,eAAe,EAAE,GAAG;IACpB,kBAAkB,EAAE,CAAC;IACrB,gBAAgB,EAAE,EAAE;IACpB,gBAAgB,EAAE,IAAI;CACvB,CAAC;AAEF,8EAA8E;AAC9E,mEAAmE;AACnE,8EAA8E;AAE9E,MAAM,mBAAmB,GAAG,IAAI,CAAC,OAAO,CACtC,IAAI,CAAC,MAAM,CAAC;IACV,oBAAoB,EAAE,IAAI,CAAC,MAAM,EAAE;IACnC,2BAA2B,EAAE,IAAI,CAAC,MAAM,EAAE;IAC1C,cAAc,EAAE,IAAI,CAAC,MAAM,EAAE;IAC7B,aAAa,EAAE,IAAI,CAAC,MAAM,EAAE;IAC5B,mBAAmB,EAAE,IAAI,CAAC,MAAM,EAAE;IAClC,KAAK,EAAE,IAAI,CAAC,MAAM,EAAE;IACpB,eAAe,EAAE,IAAI,CAAC,MAAM,EAAE;IAC9B,kBAAkB,EAAE,IAAI,CAAC,MAAM,EAAE;IACjC,gBAAgB,EAAE,IAAI,CAAC,MAAM,EAAE;IAC/B,gBAAgB,EAAE,IAAI,CAAC,MAAM,EAAE;CAChC,CAAC,CACH,CAAC;AAIF,8EAA8E;AAC9E,aAAa;AACb,8EAA8E;AAE9E;;;;GAIG;AACH,MAAM,UAAU,UAAU;IACxB,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,CAAC;QAChC,OAAO,EAAE,GAAG,cAAc,EAAE,CAAC;IAC/B,CAAC;IAED,IAAI,GAAW,CAAC;IAChB,IAAI,CAAC;QACH,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,WAAW,EAAE,OAAO,CAAW,CAAC;IACxD,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO,CAAC,IAAI,CAAC,wDAAwD,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACpF,OAAO,EAAE,GAAG,cAAc,EAAE,CAAC;IAC/B,CAAC;IAED,IAAI,MAAe,CAAC;IACpB,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;IAC3B,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO,CAAC,IAAI,CACV,yDAAyD,MAAM,CAAC,GAAG,CAAC,mBAAmB,CACxF,CAAC;QACF,OAAO,EAAE,GAAG,cAAc,EAAE,CAAC;IAC/B,CAAC;IAED,yEAAyE;IACzE,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,mBAAmB,EAAE,MAAM,CAAkB,CAAC;IAE1E,OAAO,EAAE,GAAG,cAAc,EAAE,GAAG,OAAO,EAAE,CAAC;AAC3C,CAAC"}
+{"version":3,"file":"config.js","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,IAAI,EAAe,MAAM,mBAAmB,CAAC;AACtD,OAAO,EAAE,KAAK,EAAE,MAAM,yBAAyB,CAAC;AAGhD,8EAA8E;AAC9E,YAAY;AACZ,8EAA8E;AAE9E;;;GAGG;AACH,MAAM,CAAC,MAAM,aAAa,GAA2B;IACnD,GAAG,EAAE,mCAAmC;IACxC,OAAO,EAAE,kCAAkC;IAC3C,SAAS,EAAE,8BAA8B;IACzC,QAAQ,EAAE,qCAAqC;IAC/C,UAAU,EAAE,qCAAqC;IACjD,GAAG,EAAE,iBAAiB;IACtB,MAAM,EAAE,kCAAkC;IAC1C,QAAQ,EAAE,iDAAiD;IAC3D,WAAW,EAAE,0BAA0B;IACvC,aAAa,EAAE,qCAAqC;CACrD,CAAC;AAEF,MAAM,CAAC,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAClC,EAAE,CAAC,OAAO,EAAE,EACZ,KAAK,EACL,qBAAqB,EACrB,aAAa,CACd,CAAC;AAEF,MAAM,CAAC,MAAM,cAAc,GAAW;IACpC,oBAAoB,EAAE,CAAC;IACvB,2BAA2B,EAAE,EAAE;IAC/B,cAAc,EAAE,GAAG;IACnB,aAAa,EAAE,EAAE;IACjB,mBAAmB,EAAE,IAAI;IACzB,KAAK,EAAE,kBAAkB;IACzB,eAAe,EAAE,GAAG;IACpB,kBAAkB,EAAE,CAAC;IACrB,gBAAgB,EAAE,EAAE;IACpB,gBAAgB,EAAE,IAAI;CACvB,CAAC;AAEF,8EAA8E;AAC9E,mEAAmE;AACnE,8EAA8E;AAE9E,MAAM,mBAAmB,GAAG,IAAI,CAAC,OAAO,CACtC,IAAI,CAAC,MAAM,CAAC;IACV,oBAAoB,EAAE,IAAI,CAAC,MAAM,EAAE;IACnC,2BAA2B,EAAE,IAAI,CAAC,MAAM,EAAE;IAC1C,cAAc,EAAE,IAAI,CAAC,MAAM,EAAE;IAC7B,aAAa,EAAE,IAAI,CAAC,MAAM,EAAE;IAC5B,mBAAmB,EAAE,IAAI,CAAC,MAAM,EAAE;IAClC,KAAK,EAAE,IAAI,CAAC,MAAM,EAAE;IACpB,eAAe,EAAE,IAAI,CAAC,MAAM,EAAE;IAC9B,kBAAkB,EAAE,IAAI,CAAC,MAAM,EAAE;IACjC,gBAAgB,EAAE,IAAI,CAAC,MAAM,EAAE;IAC/B,gBAAgB,EAAE,IAAI,CAAC,MAAM,EAAE;IAC/B,QAAQ,EAAE,IAAI,CAAC,MAAM,EAAE;CACxB,CAAC,CACH,CAAC;AAIF,8EAA8E;AAC9E,aAAa;AACb,8EAA8E;AAE9E;;;;GAIG;AACH,MAAM,UAAU,UAAU;IACxB,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,CAAC;QAChC,OAAO,EAAE,GAAG,cAAc,EAAE,CAAC;IAC/B,CAAC;IAED,IAAI,GAAW,CAAC;IAChB,IAAI,CAAC;QACH,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,WAAW,EAAE,OAAO,CAAW,CAAC;IACxD,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO,CAAC,IAAI,CAAC,wDAAwD,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACpF,OAAO,EAAE,GAAG,cAAc,EAAE,CAAC;IAC/B,CAAC;IAED,IAAI,MAAe,CAAC;IACpB,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;IAC3B,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO,CAAC,IAAI,CACV,yDAAyD,MAAM,CAAC,GAAG,CAAC,mBAAmB,CACxF,CAAC;QACF,OAAO,EAAE,GAAG,cAAc,EAAE,CAAC;IAC/B,CAAC;IAED,yEAAyE;IACzE,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,mBAAmB,EAAE,MAAM,CAAkB,CAAC;IAE1E,OAAO,EAAE,GAAG,cAAc,EAAE,GAAG,OAAO,EAAE,CAAC;AAC3C,CAAC"}

package/dist/types.d.ts

@@ -70,5 +70,6 @@ export interface Config {
     active_hours_start: number;
     active_hours_end: number;
     max_idle_seconds: number;
+    log_path?: string;
 }
 //# sourceMappingURL=types.d.ts.map

package/dist/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAMH,MAAM,MAAM,gBAAgB,GACxB,YAAY,GACZ,eAAe,GACf,aAAa,GACb,WAAW,GACX,YAAY,GACZ,UAAU,GACV,WAAW,GACX,iBAAiB,GACjB,cAAc,CAAC;AAEnB,MAAM,WAAW,WAAW;IAC1B,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,gBAAgB,CAAC;IACxB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC5B,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,mBAAmB,CAAC,EAAE,MAAM,CAAC;CAC9B;AAMD,MAAM,MAAM,aAAa,GAAG,SAAS,GAAG,QAAQ,CAAC;AACjD,MAAM,MAAM,cAAc,GAAG,UAAU,GAAG,WAAW,CAAC;AAEtD,MAAM,WAAW,QAAQ;IACvB,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,cAAc,CAAC;IACvB,KAAK,EAAE,aAAa,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,eAAe,EAAE,MAAM,CAAC;IACxB,kBAAkB,EAAE,MAAM,CAAC;IAC3B,cAAc,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;IACpB,mBAAmB,CAAC,EAAE,OAAO,CAAC;CAC/B;AAMD,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;CACnB;AAMD,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,MAAM;IACrB,oBAAoB,EAAE,MAAM,CAAC;IAC7B,2BAA2B,EAAE,MAAM,CAAC;IACpC,cAAc,EAAE,MAAM,CAAC;IACvB,aAAa,EAAE,MAAM,CAAC;IACtB,mBAAmB,EAAE,MAAM,CAAC;IAC5B,KAAK,EAAE,MAAM,CAAC;IACd,eAAe,EAAE,MAAM,CAAC;IACxB,kBAAkB,EAAE,MAAM,CAAC;IAC3B,gBAAgB,EAAE,MAAM,CAAC;IACzB,gBAAgB,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pi-continuous-learning",
-  "version": "0.4.0",
+  "version": "0.5.0",
   "description": "A Pi extension that observes coding sessions and distills patterns into reusable instincts.",
   "type": "module",
   "license": "MIT",

package/src/cli/analyze-logger.ts

@@ -0,0 +1,209 @@
+/**
+ * Structured logging for the background analyzer CLI.
+ * Writes to a configurable log file (default: ~/.pi/continuous-learning/analyzer.log).
+ * Each line is a JSON object for easy parsing and grep-ability.
+ *
+ * Log levels: info, warn, error
+ * Never throws - all I/O failures fall back to stderr.
+ */
+
+import { appendFileSync, mkdirSync, renameSync, statSync } from "node:fs";
+import { dirname } from "node:path";
+import { join } from "node:path";
+import { getBaseDir } from "../storage.js";
+
+// ---------------------------------------------------------------------------
+// Constants
+// ---------------------------------------------------------------------------
+
+const DEFAULT_LOG_FILENAME = "analyzer.log";
+const MAX_LOG_SIZE_BYTES = 10 * 1024 * 1024; // 10 MB - rotate beyond this
+
+// ---------------------------------------------------------------------------
+// Types
+// ---------------------------------------------------------------------------
+
+type LogLevel = "info" | "warn" | "error";
+
+interface LogEntry {
+  readonly timestamp: string;
+  readonly level: LogLevel;
+  readonly message: string;
+  readonly [key: string]: unknown;
+}
+
+export interface ProjectRunStats {
+  readonly project_id: string;
+  readonly project_name: string;
+  readonly duration_ms: number;
+  readonly observations_processed: number;
+  readonly observations_total: number;
+  readonly instincts_created: number;
+  readonly instincts_updated: number;
+  readonly instincts_deleted: number;
+  readonly tokens_input: number;
+  readonly tokens_output: number;
+  readonly tokens_cache_read: number;
+  readonly tokens_cache_write: number;
+  readonly tokens_total: number;
+  readonly cost_usd: number;
+  readonly model: string;
+  readonly skipped_reason?: string;
+}
+
+export interface RunSummary {
+  readonly total_duration_ms: number;
+  readonly projects_processed: number;
+  readonly projects_skipped: number;
+  readonly projects_errored: number;
+  readonly projects_total: number;
+  readonly total_tokens: number;
+  readonly total_cost_usd: number;
+  readonly total_instincts_created: number;
+  readonly total_instincts_updated: number;
+  readonly total_instincts_deleted: number;
+  readonly project_stats: readonly ProjectRunStats[];
+}
+
+// ---------------------------------------------------------------------------
+// Logger
+// ---------------------------------------------------------------------------
+
+export class AnalyzeLogger {
+  private readonly logPath: string;
+
+  constructor(logPath?: string) {
+    this.logPath = logPath ?? join(getBaseDir(), DEFAULT_LOG_FILENAME);
+    this.ensureLogDir();
+  }
+
+  getLogPath(): string {
+    return this.logPath;
+  }
+
+  info(message: string, data?: Record<string, unknown>): void {
+    this.write("info", message, data);
+  }
+
+  warn(message: string, data?: Record<string, unknown>): void {
+    this.write("warn", message, data);
+  }
+
+  error(message: string, error?: unknown, data?: Record<string, unknown>): void {
+    const errorData: Record<string, unknown> = { ...data };
+    if (error instanceof Error) {
+      errorData.error_message = error.message;
+      errorData.error_stack = error.stack;
+    } else if (error !== undefined) {
+      errorData.error_message = String(error);
+    }
+    this.write("error", message, errorData);
+  }
+
+  /** Log the start of a full analyzer run */
+  runStart(projectCount: number): void {
+    this.info("Analyzer run started", {
+      event: "run_start",
+      project_count: projectCount,
+      pid: process.pid,
+    });
+  }
+
+  /** Log that a project was skipped (with reason) */
+  projectSkipped(projectId: string, projectName: string, reason: string): void {
+    this.info(`Skipped ${projectName}`, {
+      event: "project_skipped",
+      project_id: projectId,
+      project_name: projectName,
+      reason,
+    });
+  }
+
+  /** Log the start of a project analysis */
+  projectStart(projectId: string, projectName: string, newObservations: number, totalObservations: number): void {
+    this.info(`Processing ${projectName}`, {
+      event: "project_start",
+      project_id: projectId,
+      project_name: projectName,
+      new_observations: newObservations,
+      total_observations: totalObservations,
+    });
+  }
+
+  /** Log per-project results after analysis completes */
+  projectComplete(stats: ProjectRunStats): void {
+    const durationSec = (stats.duration_ms / 1000).toFixed(1);
+    const costFormatted = stats.cost_usd.toFixed(4);
+    this.info(
+      `Completed ${stats.project_name} in ${durationSec}s - ` +
+      `tokens: ${stats.tokens_total}, cost: $${costFormatted}, ` +
+      `instincts: +${stats.instincts_created} ~${stats.instincts_updated} -${stats.instincts_deleted}`,
+      { event: "project_complete", ...stats }
+    );
+  }
+
+  /** Log a project that errored during analysis */
+  projectError(projectId: string, projectName: string, error: unknown): void {
+    this.error(`Error processing ${projectName}`, error, {
+      event: "project_error",
+      project_id: projectId,
+      project_name: projectName,
+    });
+  }
+
+  /** Log the full run summary */
+  runComplete(summary: RunSummary): void {
+    const durationSec = (summary.total_duration_ms / 1000).toFixed(1);
+    const costFormatted = summary.total_cost_usd.toFixed(4);
+    this.info(
+      `Run complete in ${durationSec}s - ` +
+      `${summary.projects_processed}/${summary.projects_total} projects processed, ` +
+      `${summary.projects_skipped} skipped, ${summary.projects_errored} errored - ` +
+      `tokens: ${summary.total_tokens}, cost: $${costFormatted}, ` +
+      `instincts: +${summary.total_instincts_created} ~${summary.total_instincts_updated} -${summary.total_instincts_deleted}`,
+      { event: "run_complete", ...summary }
+    );
+  }
+
+  // -------------------------------------------------------------------------
+  // Internal
+  // -------------------------------------------------------------------------
+
+  private ensureLogDir(): void {
+    try {
+      mkdirSync(dirname(this.logPath), { recursive: true });
+    } catch {
+      // Best effort
+    }
+  }
+
+  private write(level: LogLevel, message: string, data?: Record<string, unknown>): void {
+    const entry: LogEntry = {
+      timestamp: new Date().toISOString(),
+      level,
+      message,
+      ...data,
+    };
+
+    const line = JSON.stringify(entry) + "\n";
+
+    try {
+      this.rotateIfNeeded();
+      appendFileSync(this.logPath, line, "utf-8");
+    } catch {
+      // Fall back to stderr - never lose log entries entirely
+      process.stderr.write(`[analyze] ${line}`);
+    }
+  }
+
+  private rotateIfNeeded(): void {
+    try {
+      const stat = statSync(this.logPath);
+      if (stat.size > MAX_LOG_SIZE_BYTES) {
+        renameSync(this.logPath, this.logPath + ".old");
+      }
+    } catch {
+      // File doesn't exist yet or stat failed - fine
+    }
+  }
+}

package/src/cli/analyze.ts

@@ -37,13 +37,14 @@ import {
 import { readAgentsMd } from "../agents-md.js";
 import { homedir } from "node:os";
 import type { InstalledSkill } from "../types.js";
+import { AnalyzeLogger, type ProjectRunStats, type RunSummary } from "./analyze-logger.js";
 
 // ---------------------------------------------------------------------------
-// Lockfile guard — ensures only one instance runs at a time
+// Lockfile guard - ensures only one instance runs at a time
 // ---------------------------------------------------------------------------
 
 const LOCKFILE_NAME = "analyze.lock";
-const LOCK_STALE_MS = 10 * 60 * 1000; // 10 minutes — stale lock threshold
+const LOCK_STALE_MS = 10 * 60 * 1000; // 10 minutes - stale lock threshold
 
 function getLockfilePath(baseDir: string): string {
   return join(baseDir, LOCKFILE_NAME);
@@ -64,12 +65,12 @@ function acquireLock(baseDir: string): boolean {
         if (age < LOCK_STALE_MS) {
           return false; // Process alive and lock is fresh
         }
-        // Process alive but lock is stale — treat as abandoned
+        // Process alive but lock is stale - treat as abandoned
       } catch {
-        // Process is dead — lock is orphaned, safe to take over
+        // Process is dead - lock is orphaned, safe to take over
       }
     } catch {
-      // Malformed lockfile — remove and proceed
+      // Malformed lockfile - remove and proceed
     }
   }
 
@@ -86,7 +87,7 @@ function releaseLock(baseDir: string): void {
   try {
     if (existsSync(lockPath)) unlinkSync(lockPath);
   } catch {
-    // Best effort — don't crash on cleanup
+    // Best effort - don't crash on cleanup
   }
 }
 
@@ -96,13 +97,79 @@ function releaseLock(baseDir: string): void {
 
 const DEFAULT_TIMEOUT_MS = 5 * 60 * 1000; // 5 minutes total
 
-function startGlobalTimeout(timeoutMs: number): void {
+function startGlobalTimeout(timeoutMs: number, logger: AnalyzeLogger): void {
   setTimeout(() => {
-    console.error("[analyze] Global timeout reached. Exiting.");
+    logger.error("Global timeout reached, forcing exit");
     process.exit(2);
   }, timeoutMs).unref();
 }
 
+// ---------------------------------------------------------------------------
+// Instinct operation tracking
+// ---------------------------------------------------------------------------
+
+interface InstinctOpCounts {
+  created: number;
+  updated: number;
+  deleted: number;
+}
+
+/**
+ * Wraps instinct tools to count create/update/delete operations.
+ * Returns new tool instances that increment the provided counts.
+ */
+function wrapInstinctToolsWithTracking(
+  projectId: string,
+  projectName: string,
+  baseDir: string,
+  counts: InstinctOpCounts
+) {
+  const writeTool = createInstinctWriteTool(projectId, projectName, baseDir);
+  const deleteTool = createInstinctDeleteTool(projectId, baseDir);
+
+  const trackedWrite = {
+    ...writeTool,
+    async execute(
+      toolCallId: string,
+      params: Parameters<typeof writeTool.execute>[1],
+      signal: AbortSignal | undefined,
+      onUpdate: unknown,
+      ctx: unknown
+    ) {
+      const result = await writeTool.execute(toolCallId, params, signal, onUpdate, ctx);
+      const details = result.details as { action?: string } | undefined;
+      if (details?.action === "created") {
+        counts.created++;
+      } else {
+        counts.updated++;
+      }
+      return result;
+    },
+  };
+
+  const trackedDelete = {
+    ...deleteTool,
+    async execute(
+      toolCallId: string,
+      params: Parameters<typeof deleteTool.execute>[1],
+      signal: AbortSignal | undefined,
+      onUpdate: unknown,
+      ctx: unknown
+    ) {
+      const result = await deleteTool.execute(toolCallId, params, signal, onUpdate, ctx);
+      counts.deleted++;
+      return result;
+    },
+  };
+
+  return {
+    listTool: createInstinctListTool(projectId, baseDir),
+    readTool: createInstinctReadTool(projectId, baseDir),
+    writeTool: trackedWrite,
+    deleteTool: trackedDelete,
+  };
+}
+
 // ---------------------------------------------------------------------------
 // Per-project analysis
 // ---------------------------------------------------------------------------
@@ -150,27 +217,39 @@ function hasNewObservations(projectId: string, meta: ProjectMeta, baseDir: strin
   return true;
 }
 
+interface AnalyzeResult {
+  readonly ran: boolean;
+  readonly stats?: ProjectRunStats;
+  readonly skippedReason?: string;
+}
+
 async function analyzeProject(
   project: ProjectEntry,
   config: ReturnType<typeof loadConfig>,
-  baseDir: string
-): Promise<boolean> {
+  baseDir: string,
+  logger: AnalyzeLogger
+): Promise<AnalyzeResult> {
   const meta = loadProjectMeta(project.id, baseDir);
 
-  if (!hasNewObservations(project.id, meta, baseDir)) return false;
+  if (!hasNewObservations(project.id, meta, baseDir)) {
+    return { ran: false, skippedReason: "no new observations" };
+  }
 
   const obsPath = getObservationsPath(project.id, baseDir);
   const sinceLineCount = meta.last_observation_line_count ?? 0;
   const { lines: newObsLines, totalLineCount } = tailObservationsSince(obsPath, sinceLineCount);
 
-  if (newObsLines.length === 0) return false;
+  if (newObsLines.length === 0) {
+    return { ran: false, skippedReason: "no new observation lines" };
+  }
 
   const obsCount = countObservations(project.id, baseDir);
-  if (obsCount < config.min_observations_to_analyze) return false;
+  if (obsCount < config.min_observations_to_analyze) {
+    return { ran: false, skippedReason: `below threshold (${obsCount}/${config.min_observations_to_analyze})` };
+  }
 
-  console.log(
-    `[analyze] Processing ${project.name} (${project.id}): ${newObsLines.length} new observations (${obsCount} total)`
-  );
+  const startTime = Date.now();
+  logger.projectStart(project.id, project.name, newObsLines.length, obsCount);
 
   runDecayPass(project.id, baseDir);
 
@@ -188,7 +267,7 @@ async function analyzeProject(
       description: s.description,
     }));
   } catch {
-    // Skills loading is best-effort — continue without them
+    // Skills loading is best-effort - continue without them
   }
 
   const userPrompt = buildAnalyzerUserPrompt(obsPath, instinctsDir, project, {
@@ -203,11 +282,15 @@ async function analyzeProject(
   const modelId = (config.model || DEFAULT_CONFIG.model) as Parameters<typeof getModel>[1];
   const model = getModel("anthropic", modelId);
 
+  // Track instinct operations
+  const instinctCounts: InstinctOpCounts = { created: 0, updated: 0, deleted: 0 };
+  const trackedTools = wrapInstinctToolsWithTracking(project.id, project.name, baseDir, instinctCounts);
+
   const customTools = [
-    createInstinctListTool(project.id, baseDir),
-    createInstinctReadTool(project.id, baseDir),
-    createInstinctWriteTool(project.id, project.name, baseDir),
-    createInstinctDeleteTool(project.id, baseDir),
+    trackedTools.listTool,
+    trackedTools.readTool,
+    trackedTools.writeTool,
+    trackedTools.deleteTool,
   ];
 
   const loader = new DefaultResourceLoader({
@@ -230,13 +313,37 @@ async function analyzeProject(
     session.dispose();
   }
 
+  // Collect stats after session completes
+  const sessionStats = session.getSessionStats();
+  const durationMs = Date.now() - startTime;
+
+  const stats: ProjectRunStats = {
+    project_id: project.id,
+    project_name: project.name,
+    duration_ms: durationMs,
+    observations_processed: newObsLines.length,
+    observations_total: obsCount,
+    instincts_created: instinctCounts.created,
+    instincts_updated: instinctCounts.updated,
+    instincts_deleted: instinctCounts.deleted,
+    tokens_input: sessionStats.tokens.input,
+    tokens_output: sessionStats.tokens.output,
+    tokens_cache_read: sessionStats.tokens.cacheRead,
+    tokens_cache_write: sessionStats.tokens.cacheWrite,
+    tokens_total: sessionStats.tokens.total,
+    cost_usd: sessionStats.cost,
+    model: modelId,
+  };
+
+  logger.projectComplete(stats);
+
   saveProjectMeta(
     project.id,
     { ...meta, last_analyzed_at: new Date().toISOString(), last_observation_line_count: totalLineCount },
     baseDir
   );
-  console.log(`[analyze] Completed ${project.name}`);
-  return true;
+
+  return { ran: true, stats };
 }
 
 // ---------------------------------------------------------------------------
@@ -245,35 +352,67 @@ async function analyzeProject(
 
 async function main(): Promise<void> {
   const baseDir = getBaseDir();
+  const config = loadConfig();
+  const logger = new AnalyzeLogger(config.log_path);
 
   if (!acquireLock(baseDir)) {
-    console.log("[analyze] Another instance is already running. Exiting.");
+    logger.info("Another instance is already running, exiting");
     process.exit(0);
   }
 
-  startGlobalTimeout(DEFAULT_TIMEOUT_MS);
+  startGlobalTimeout(DEFAULT_TIMEOUT_MS, logger);
+
+  const runStart = Date.now();
 
   try {
-    const config = loadConfig();
     const registry = loadProjectsRegistry(baseDir);
     const projects = Object.values(registry);
 
     if (projects.length === 0) {
-      console.log("[analyze] No projects registered. Use pi with the continuous-learning extension first.");
+      logger.info("No projects registered");
       return;
     }
 
+    logger.runStart(projects.length);
+
     let processed = 0;
+    let skipped = 0;
+    let errored = 0;
+    const allProjectStats: ProjectRunStats[] = [];
+
     for (const project of projects) {
       try {
-        const didRun = await analyzeProject(project, config, baseDir);
-        if (didRun) processed++;
+        const result = await analyzeProject(project, config, baseDir, logger);
+        if (result.ran && result.stats) {
+          processed++;
+          allProjectStats.push(result.stats);
+        } else {
+          skipped++;
+          if (result.skippedReason) {
+            logger.projectSkipped(project.id, project.name, result.skippedReason);
+          }
+        }
       } catch (err) {
-        console.error(`[analyze] Error processing ${project.name}: ${String(err)}`);
+        errored++;
+        logger.projectError(project.id, project.name, err);
       }
     }
 
-    console.log(`[analyze] Done. Processed ${processed}/${projects.length} project(s).`);
+    const summary: RunSummary = {
+      total_duration_ms: Date.now() - runStart,
+      projects_processed: processed,
+      projects_skipped: skipped,
+      projects_errored: errored,
+      projects_total: projects.length,
+      total_tokens: allProjectStats.reduce((sum, s) => sum + s.tokens_total, 0),
+      total_cost_usd: allProjectStats.reduce((sum, s) => sum + s.cost_usd, 0),
+      total_instincts_created: allProjectStats.reduce((sum, s) => sum + s.instincts_created, 0),
+      total_instincts_updated: allProjectStats.reduce((sum, s) => sum + s.instincts_updated, 0),
+      total_instincts_deleted: allProjectStats.reduce((sum, s) => sum + s.instincts_deleted, 0),
+      project_stats: allProjectStats,
+    };
+
+    logger.runComplete(summary);
   } finally {
     releaseLock(baseDir);
   }
@@ -281,6 +420,8 @@ async function main(): Promise<void> {
 
 main().catch((err) => {
   releaseLock(getBaseDir());
-  console.error(`[analyze] Fatal error: ${String(err)}`);
+  // Last-resort logging - config may not have loaded
+  const logger = new AnalyzeLogger();
+  logger.error("Fatal error", err);
   process.exit(1);
 });

package/src/config.ts

@@ -67,6 +67,7 @@ const PartialConfigSchema = Type.Partial(
     active_hours_start: Type.Number(),
     active_hours_end: Type.Number(),
     max_idle_seconds: Type.Number(),
+    log_path: Type.String(),
   })
 );
 

package/src/types.ts

@@ -102,4 +102,5 @@ export interface Config {
   active_hours_start: number; // 0-23
   active_hours_end: number; // 0-23
   max_idle_seconds: number;
+  log_path?: string; // Override analyzer log location (default: ~/.pi/continuous-learning/analyzer.log)
 }