pi-continuous-learning 0.5.1 → 0.7.0

package/README.md

@@ -57,6 +57,7 @@ To analyze observations and create/update instincts, you need to run the analyze
 | `/instinct-export` | Export instincts to a JSON file (filterable by scope/domain) |
 | `/instinct-import <path>` | Import instincts from a JSON file |
 | `/instinct-promote [id]` | Promote project instincts to global scope |
+| `/instinct-graduate` | Graduate mature instincts to AGENTS.md, skills, or commands |
 | `/instinct-projects` | List all known projects and their instinct counts |
 
 ### LLM Tools
@@ -244,6 +245,46 @@ inactive_count: 12
 Always search with grep to find relevant context before editing files.
 ```
 
+Graduated instincts include additional fields:
+
+```yaml
+---
+id: grep-before-edit
+# ...other fields...
+graduated_to: agents-md
+graduated_at: "2026-03-27T12:00:00.000Z"
+---
+```
+
+## Instinct Quality Control
+
+Every instinct write (from the LLM tools or the background analyzer) is validated and deduplicated before being saved.
+
+### Content Validation
+
+| Rule | Details |
+|---|---|
+| Non-empty fields | `action` and `trigger` cannot be `undefined`, `null`, `"null"`, `"none"`, or empty |
+| Minimum length | Both fields must be >= 10 characters |
+| Known domain | `domain` must be in the known set: `git`, `testing`, `debugging`, `workflow`, `typescript`, `javascript`, `python`, `go`, `css`, `design`, `security`, `performance`, `documentation`, `react`, `node`, `database`, `api`, `devops`, `architecture`, or `other` |
+| Verb heuristic | `action` should start with an imperative verb - a warning is logged but the write is not rejected |
+
+### Semantic Deduplication
+
+Before a new instinct is created, a Jaccard similarity check runs against all existing instincts. Tokenize `trigger + action`, compute `|intersection| / |union|`, and block the write if any existing instinct scores >= 0.6.
+
+This prevents near-duplicate instincts from accumulating. When a similar instinct exists, the LLM is told to update the existing one instead.
+
+### Analyzer Quality Tiers
+
+The background analyzer is instructed to classify patterns before recording them:
+
+- **Project Conventions** (Tier 1): Project-specific patterns like "use Result<T,E> for errors in this codebase" → record as project-scoped instinct
+- **Workflow Patterns** (Tier 2): Universal multi-step workflows → record as global-scoped instinct
+- **Generic Agent Behavior** (Tier 3): Read-before-edit, clarify-before-implement, check-errors-after-tool-calls → **skip entirely**, these are fundamental behaviors not learned patterns
+
+The analyzer also checks AGENTS.md content before creating instincts - if a pattern is already covered by AGENTS.md, it is skipped.
+
 ## Confidence Scoring
 
 Confidence comes from two sources:
@@ -263,6 +304,39 @@ Confidence comes from two sources:
 
 This means an instinct observed 20 times but consistently contradicted in practice will lose confidence. Frequency alone doesn't equal correctness.
 
+## Instinct Graduation
+
+Instincts are designed to be short-lived - they should graduate into permanent knowledge within a few weeks. The graduation pipeline (`/instinct-graduate`) handles this lifecycle:
+
+```
+Observation -> Instinct (days) -> AGENTS.md / Skill / Command (1-2 weeks)
+```
+
+### Graduation Targets
+
+| Target | When | What happens |
+|--------|------|--------------|
+| **AGENTS.md** | Single mature instinct | Appended as a guideline entry to your project or global AGENTS.md |
+| **Skill** | 3+ related instincts in the same domain | Scaffolded into a `SKILL.md` file |
+| **Command** | 3+ workflow instincts in the same domain | Scaffolded into a slash command specification |
+
+### Maturity Criteria
+
+An instinct qualifies for graduation when all of these are met:
+- Age >= 7 days
+- Confidence >= 0.75
+- Confirmed >= 3 times
+- Contradicted <= 1 time
+- Not a duplicate of existing AGENTS.md content
+
+### TTL Enforcement
+
+Instincts that don't graduate within 28 days are subject to TTL enforcement:
+- **Confidence < 0.3**: Deleted outright
+- **Confidence >= 0.3**: Aggressively decayed (confidence halved, flagged for removal)
+
+Graduated instincts are tracked with `graduated_to` and `graduated_at` fields so they aren't left as duplicates of the knowledge they graduated into.
+
 ## Updating
 
 ```bash
@@ -296,12 +370,16 @@ Only include the fields you want to change — missing fields use the defaults a
 
 | Field | Default | Description |
 |-------|---------|-------------|
+| `run_interval_minutes` | 5 | How often the analyzer is expected to run (informational, used for decay calculations) |
 | `min_observations_to_analyze` | 20 | Minimum observations before analysis triggers |
 | `min_confidence` | 0.5 | Instincts below this are not injected into prompts |
 | `max_instincts` | 20 | Maximum instincts injected per turn |
 | `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 |
+| `active_hours_start` | 8 | Hour (0-23) at which the active observation window starts |
+| `active_hours_end` | 23 | Hour (0-23) at which the active observation window ends |
+| `max_idle_seconds` | 1800 | Seconds of inactivity before a session is considered idle |
 | `log_path` | `~/.pi/continuous-learning/analyzer.log` | Path to the analyzer log file |
 
 ## Storage

package/dist/agents-md.d.ts

@@ -1,7 +1,8 @@
 /**
- * Utility for reading AGENTS.md files.
- * Provides a safe wrapper around filesystem access that returns null on any failure.
+ * Utility for reading and writing AGENTS.md files.
+ * Provides safe wrappers around filesystem access.
  */
+import type { Instinct } from "./types.js";
 /**
  * Reads an AGENTS.md file and returns its content.
  * Returns null if the file does not exist or cannot be read.
@@ -9,4 +10,24 @@
  * @param filePath - Absolute path to the AGENTS.md file
  */
 export declare function readAgentsMd(filePath: string): string | null;
+/**
+ * Formats an instinct as an AGENTS.md section entry.
+ * Produces a markdown block with the instinct title as heading and
+ * trigger/action as content.
+ */
+export declare function formatInstinctAsAgentsMdEntry(instinct: Instinct): string;
+/**
+ * Generates a complete AGENTS.md diff showing proposed additions.
+ * Returns the full new content that would result from appending the entries.
+ */
+export declare function generateAgentsMdDiff(currentContent: string | null, instincts: Instinct[]): string;
+/**
+ * Appends graduated instinct entries to an AGENTS.md file.
+ * Creates the file and parent directories if they don't exist.
+ *
+ * @param filePath - Absolute path to AGENTS.md
+ * @param instincts - Instincts to append as entries
+ * @returns The new file content that was written
+ */
+export declare function appendToAgentsMd(filePath: string, instincts: Instinct[]): string;
 //# sourceMappingURL=agents-md.d.ts.map

package/dist/agents-md.d.ts.map

@@ -1 +1 @@
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package/dist/agents-md.js

@@ -1,8 +1,9 @@
 /**
- * Utility for reading AGENTS.md files.
- * Provides a safe wrapper around filesystem access that returns null on any failure.
+ * Utility for reading and writing AGENTS.md files.
+ * Provides safe wrappers around filesystem access.
  */
-import { existsSync, readFileSync } from "node:fs";
+import { existsSync, readFileSync, writeFileSync, mkdirSync } from "node:fs";
+import { dirname } from "node:path";
 /**
  * Reads an AGENTS.md file and returns its content.
  * Returns null if the file does not exist or cannot be read.
@@ -20,4 +21,58 @@ export function readAgentsMd(filePath) {
         return null;
     }
 }
+/**
+ * Formats an instinct as an AGENTS.md section entry.
+ * Produces a markdown block with the instinct title as heading and
+ * trigger/action as content.
+ */
+export function formatInstinctAsAgentsMdEntry(instinct) {
+    const lines = [
+        `### ${instinct.title}`,
+        "",
+        `**When:** ${instinct.trigger}`,
+        "",
+        instinct.action,
+        "",
+    ];
+    return lines.join("\n");
+}
+/**
+ * Generates a complete AGENTS.md diff showing proposed additions.
+ * Returns the full new content that would result from appending the entries.
+ */
+export function generateAgentsMdDiff(currentContent, instincts) {
+    const entries = instincts.map(formatInstinctAsAgentsMdEntry);
+    const graduatedSection = [
+        "",
+        "## Graduated Instincts",
+        "",
+        ...entries,
+    ].join("\n");
+    if (currentContent === null || currentContent.trim().length === 0) {
+        return `# Project Guidelines\n${graduatedSection}\n`;
+    }
+    // If the section already exists, append to it; otherwise add a new section
+    if (currentContent.includes("## Graduated Instincts")) {
+        return `${currentContent.trimEnd()}\n\n${entries.join("\n")}\n`;
+    }
+    return `${currentContent.trimEnd()}\n${graduatedSection}\n`;
+}
+/**
+ * Appends graduated instinct entries to an AGENTS.md file.
+ * Creates the file and parent directories if they don't exist.
+ *
+ * @param filePath - Absolute path to AGENTS.md
+ * @param instincts - Instincts to append as entries
+ * @returns The new file content that was written
+ */
+export function appendToAgentsMd(filePath, instincts) {
+    if (instincts.length === 0)
+        return readAgentsMd(filePath) ?? "";
+    const currentContent = readAgentsMd(filePath);
+    const newContent = generateAgentsMdDiff(currentContent, instincts);
+    mkdirSync(dirname(filePath), { recursive: true });
+    writeFileSync(filePath, newContent, "utf-8");
+    return newContent;
+}
 //# sourceMappingURL=agents-md.js.map

package/dist/agents-md.js.map

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package/dist/cli/analyze-single-shot.d.ts

@@ -0,0 +1,62 @@
+/**
+ * Single-shot (non-agentic) analyzer core.
+ *
+ * Replaces the multi-turn agentic session with a single complete() call.
+ * The model receives all current instincts inline and returns a JSON change-set.
+ * Changes are applied client-side, eliminating the ~16x cache-read multiplier.
+ */
+import type { AssistantMessage, Context } from "@mariozechner/pi-ai";
+import { complete } from "@mariozechner/pi-ai";
+import type { Instinct } from "../types.js";
+export interface InstinctChangePayload {
+    id: string;
+    title: string;
+    trigger: string;
+    action: string;
+    confidence: number;
+    domain: string;
+    scope: "project" | "global";
+    observation_count?: number;
+    confirmed_count?: number;
+    contradicted_count?: number;
+    inactive_count?: number;
+    evidence?: string[];
+}
+export interface InstinctChange {
+    action: "create" | "update" | "delete";
+    instinct?: InstinctChangePayload;
+    /** For delete: the instinct ID to remove. */
+    id?: string;
+    /** For delete: the scope to target. */
+    scope?: "project" | "global";
+}
+export interface SingleShotResult {
+    changes: InstinctChange[];
+    message: AssistantMessage;
+}
+/**
+ * Parses the model's raw text response into an array of InstinctChange.
+ * Strips markdown code fences if present. Throws on invalid JSON or schema.
+ */
+export declare function parseChanges(raw: string): InstinctChange[];
+/**
+ * Builds a full Instinct from a create/update change.
+ * Returns null for delete changes, changes with missing instinct data,
+ * invalid fields, or semantically duplicate actions.
+ *
+ * @param change        - The change to apply
+ * @param existing      - The existing instinct with this ID, if any
+ * @param projectId     - Project ID for scoping
+ * @param allInstincts  - All current instincts, used for dedup check on creates
+ */
+export declare function buildInstinctFromChange(change: InstinctChange, existing: Instinct | null, projectId: string, allInstincts?: Instinct[]): Instinct | null;
+/**
+ * Formats existing instincts as serialized markdown blocks for inline context.
+ */
+export declare function formatInstinctsForPrompt(instincts: Instinct[]): string;
+/**
+ * Runs a single complete() call with the provided context.
+ * Returns parsed changes and the raw AssistantMessage (for usage stats).
+ */
+export declare function runSingleShot(context: Context, model: Parameters<typeof complete>[0], apiKey: string, signal?: AbortSignal): Promise<SingleShotResult>;
+//# sourceMappingURL=analyze-single-shot.d.ts.map

package/dist/cli/analyze-single-shot.d.ts.map

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package/dist/cli/analyze-single-shot.js

@@ -0,0 +1,105 @@
+import { complete } from "@mariozechner/pi-ai";
+import { serializeInstinct } from "../instinct-parser.js";
+import { validateInstinct, findSimilarInstinct } from "../instinct-validator.js";
+/**
+ * Parses the model's raw text response into an array of InstinctChange.
+ * Strips markdown code fences if present. Throws on invalid JSON or schema.
+ */
+export function parseChanges(raw) {
+    const stripped = raw
+        .replace(/^```(?:json)?\s*/i, "")
+        .replace(/\s*```\s*$/, "")
+        .trim();
+    let parsed;
+    try {
+        parsed = JSON.parse(stripped);
+    }
+    catch (e) {
+        throw new Error(`Analyzer returned invalid JSON: ${String(e)}\nRaw: ${raw.slice(0, 200)}`);
+    }
+    if (typeof parsed !== "object" ||
+        parsed === null ||
+        !Array.isArray(parsed.changes)) {
+        throw new Error(`Analyzer response missing 'changes' array. Got: ${JSON.stringify(parsed).slice(0, 200)}`);
+    }
+    return parsed.changes;
+}
+/**
+ * Builds a full Instinct from a create/update change.
+ * Returns null for delete changes, changes with missing instinct data,
+ * invalid fields, or semantically duplicate actions.
+ *
+ * @param change        - The change to apply
+ * @param existing      - The existing instinct with this ID, if any
+ * @param projectId     - Project ID for scoping
+ * @param allInstincts  - All current instincts, used for dedup check on creates
+ */
+export function buildInstinctFromChange(change, existing, projectId, allInstincts = []) {
+    if (change.action === "delete" || !change.instinct) {
+        return null;
+    }
+    const payload = change.instinct;
+    const validation = validateInstinct({
+        action: payload.action,
+        trigger: payload.trigger,
+        domain: payload.domain,
+    });
+    if (!validation.valid) {
+        return null;
+    }
+    // On create, reject if semantically similar to an existing instinct (skip self on update)
+    if (change.action === "create") {
+        const similar = findSimilarInstinct({ trigger: payload.trigger, action: payload.action }, allInstincts, payload.id);
+        if (similar) {
+            return null;
+        }
+    }
+    const now = new Date().toISOString();
+    return {
+        id: payload.id,
+        title: payload.title,
+        trigger: payload.trigger,
+        action: payload.action,
+        confidence: Math.max(0.1, Math.min(0.9, payload.confidence)),
+        domain: payload.domain,
+        scope: payload.scope,
+        source: "personal",
+        ...(payload.scope === "project" ? { project_id: projectId } : {}),
+        created_at: existing?.created_at ?? now,
+        updated_at: now,
+        observation_count: payload.observation_count ?? 1,
+        confirmed_count: payload.confirmed_count ?? 0,
+        contradicted_count: payload.contradicted_count ?? 0,
+        inactive_count: payload.inactive_count ?? 0,
+        ...(payload.evidence !== undefined ? { evidence: payload.evidence } : {}),
+    };
+}
+/**
+ * Formats existing instincts as serialized markdown blocks for inline context.
+ */
+export function formatInstinctsForPrompt(instincts) {
+    if (instincts.length === 0) {
+        return "(no existing instincts)";
+    }
+    return instincts.map((i) => serializeInstinct(i)).join("\n---\n");
+}
+/**
+ * Runs a single complete() call with the provided context.
+ * Returns parsed changes and the raw AssistantMessage (for usage stats).
+ */
+export async function runSingleShot(context, model, apiKey, signal) {
+    const opts = { apiKey };
+    if (signal !== undefined)
+        opts.signal = signal;
+    const message = await complete(model, context, opts);
+    const textContent = message.content
+        .filter((c) => c.type === "text")
+        .map((c) => c.text)
+        .join("");
+    if (!textContent.trim()) {
+        throw new Error("Analyzer returned empty response");
+    }
+    const changes = parseChanges(textContent);
+    return { changes, message };
+}
+//# sourceMappingURL=analyze-single-shot.js.map

package/dist/cli/analyze-single-shot.js.map

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

@@ -1,15 +1,18 @@
 #!/usr/bin/env node
 import { existsSync, readFileSync, statSync, writeFileSync, unlinkSync, } from "node:fs";
 import { join } from "node:path";
-import { createAgentSession, SessionManager, AuthStorage, ModelRegistry, DefaultResourceLoader, } from "@mariozechner/pi-coding-agent";
+import { AuthStorage } from "@mariozechner/pi-coding-agent";
 import { getModel } from "@mariozechner/pi-ai";
 import { loadConfig, DEFAULT_CONFIG } from "../config.js";
-import { getBaseDir, getProjectsRegistryPath, getObservationsPath, getProjectDir, } from "../storage.js";
+import { getBaseDir, getProjectsRegistryPath, getObservationsPath, getProjectDir, getProjectInstinctsDir, getGlobalInstinctsDir, } from "../storage.js";
 import { countObservations } from "../observations.js";
 import { runDecayPass } from "../instinct-decay.js";
-import { buildAnalyzerUserPrompt, tailObservationsSince } from "../prompts/analyzer-user.js";
-import { buildAnalyzerSystemPrompt } from "./analyze-prompt.js";
-import { createInstinctListTool, createInstinctReadTool, createInstinctWriteTool, createInstinctDeleteTool, } from "../instinct-tools.js";
+import { runCleanupPass } from "../instinct-cleanup.js";
+import { tailObservationsSince } from "../prompts/analyzer-user.js";
+import { buildSingleShotSystemPrompt } from "../prompts/analyzer-system-single-shot.js";
+import { buildSingleShotUserPrompt } from "../prompts/analyzer-user-single-shot.js";
+import { runSingleShot, buildInstinctFromChange, } from "./analyze-single-shot.js";
+import { loadProjectInstincts, loadGlobalInstincts, saveInstinct, } from "../instinct-store.js";
 import { readAgentsMd } from "../agents-md.js";
 import { homedir } from "node:os";
 import { AnalyzeLogger } from "./analyze-logger.js";
@@ -28,7 +31,6 @@ function acquireLock(baseDir) {
             const content = readFileSync(lockPath, "utf-8");
             const lock = JSON.parse(content);
             const age = Date.now() - new Date(lock.started_at).getTime();
-            // Check if the owning process is still alive
             try {
                 process.kill(lock.pid, 0); // signal 0 = existence check, no actual signal
                 if (age < LOCK_STALE_MS) {
@@ -67,42 +69,6 @@ function startGlobalTimeout(timeoutMs, logger) {
         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))
@@ -148,18 +114,22 @@ async function analyzeProject(project, config, baseDir, logger) {
     }
     const obsPath = getObservationsPath(project.id, baseDir);
     const sinceLineCount = meta.last_observation_line_count ?? 0;
-    const { lines: newObsLines, totalLineCount } = tailObservationsSince(obsPath, sinceLineCount);
+    const { lines: newObsLines, totalLineCount, rawLineCount } = tailObservationsSince(obsPath, sinceLineCount);
     if (newObsLines.length === 0) {
-        return { ran: false, skippedReason: "no new observation lines" };
+        return { ran: false, skippedReason: "no new observation lines after preprocessing" };
     }
     const obsCount = countObservations(project.id, baseDir);
     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);
+    logger.projectStart(project.id, project.name, rawLineCount, obsCount);
+    runCleanupPass(project.id, config, baseDir);
     runDecayPass(project.id, baseDir);
-    const instinctsDir = join(getProjectDir(project.id, baseDir), "instincts", "personal");
+    // Load current instincts inline - no tool calls needed
+    const projectInstincts = loadProjectInstincts(project.id, baseDir);
+    const globalInstincts = loadGlobalInstincts(baseDir);
+    const allInstincts = [...projectInstincts, ...globalInstincts];
     const agentsMdProject = readAgentsMd(join(project.root, "AGENTS.md"));
     const agentsMdGlobal = readAgentsMd(join(homedir(), ".pi", "agent", "AGENTS.md"));
     let installedSkills = [];
@@ -174,61 +144,93 @@ async function analyzeProject(project, config, baseDir, logger) {
     catch {
         // Skills loading is best-effort - continue without them
     }
-    const userPrompt = buildAnalyzerUserPrompt(obsPath, instinctsDir, project, {
+    const userPrompt = buildSingleShotUserPrompt(project, allInstincts, newObsLines, {
         agentsMdProject,
         agentsMdGlobal,
         installedSkills,
-        observationLines: newObsLines,
     });
     const authStorage = AuthStorage.create();
-    const modelRegistry = new ModelRegistry(authStorage);
     const modelId = (config.model || DEFAULT_CONFIG.model);
     const model = getModel("anthropic", modelId);
-    // Track instinct operations
+    const apiKey = await authStorage.getApiKey("anthropic");
+    if (!apiKey) {
+        throw new Error("No Anthropic API key configured. Set via auth.json or ANTHROPIC_API_KEY.");
+    }
+    const context = {
+        systemPrompt: buildSingleShotSystemPrompt(),
+        messages: [
+            { role: "user", content: userPrompt, timestamp: Date.now() },
+        ],
+    };
+    const timeoutMs = (config.timeout_seconds ?? DEFAULT_CONFIG.timeout_seconds) * 1000;
+    const abortController = new AbortController();
+    const timeoutHandle = setTimeout(() => abortController.abort(), timeoutMs);
     const instinctCounts = { created: 0, updated: 0, deleted: 0 };
-    const trackedTools = wrapInstinctToolsWithTracking(project.id, project.name, baseDir, instinctCounts);
-    const customTools = [
-        trackedTools.listTool,
-        trackedTools.readTool,
-        trackedTools.writeTool,
-        trackedTools.deleteTool,
-    ];
-    const loader = new DefaultResourceLoader({
-        systemPromptOverride: () => buildAnalyzerSystemPrompt(),
-    });
-    await loader.reload();
-    const { session } = await createAgentSession({
-        model,
-        authStorage,
-        modelRegistry,
-        sessionManager: SessionManager.inMemory(),
-        customTools,
-        resourceLoader: loader,
-    });
+    const projectInstinctsDir = getProjectInstinctsDir(project.id, "personal", baseDir);
+    const globalInstinctsDir = getGlobalInstinctsDir("personal", baseDir);
+    let singleShotMessage;
     try {
-        await session.prompt(userPrompt);
+        const result = await runSingleShot(context, model, apiKey, abortController.signal);
+        singleShotMessage = result.message;
+        // Enforce creation rate limit: only the first N create actions per run are applied.
+        const maxNewInstincts = config.max_new_instincts_per_run ?? DEFAULT_CONFIG.max_new_instincts_per_run;
+        let createsRemaining = maxNewInstincts;
+        for (const change of result.changes) {
+            if (change.action === "delete") {
+                const id = change.id;
+                if (!id)
+                    continue;
+                const dir = change.scope === "global" ? globalInstinctsDir : projectInstinctsDir;
+                const filePath = join(dir, `${id}.md`);
+                if (existsSync(filePath)) {
+                    unlinkSync(filePath);
+                    instinctCounts.deleted++;
+                }
+            }
+            else if (change.action === "create") {
+                if (createsRemaining <= 0)
+                    continue; // rate limit reached
+                const existing = allInstincts.find((i) => i.id === change.instinct?.id) ?? null;
+                const instinct = buildInstinctFromChange(change, existing, project.id, allInstincts);
+                if (!instinct)
+                    continue;
+                const dir = instinct.scope === "global" ? globalInstinctsDir : projectInstinctsDir;
+                saveInstinct(instinct, dir);
+                instinctCounts.created++;
+                createsRemaining--;
+            }
+            else {
+                // update
+                const existing = allInstincts.find((i) => i.id === change.instinct?.id) ?? null;
+                const instinct = buildInstinctFromChange(change, existing, project.id, allInstincts);
+                if (!instinct)
+                    continue;
+                const dir = instinct.scope === "global" ? globalInstinctsDir : projectInstinctsDir;
+                saveInstinct(instinct, dir);
+                instinctCounts.updated++;
+            }
+        }
     }
     finally {
-        session.dispose();
+        clearTimeout(timeoutHandle);
     }
-    // Collect stats after session completes
-    const sessionStats = session.getSessionStats();
+    const usage = singleShotMessage.usage;
     const durationMs = Date.now() - startTime;
     const stats = {
         project_id: project.id,
         project_name: project.name,
         duration_ms: durationMs,
-        observations_processed: newObsLines.length,
+        observations_processed: rawLineCount,
         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,
+        tokens_input: usage.input,
+        tokens_output: usage.output,
+        tokens_cache_read: usage.cacheRead,
+        tokens_cache_write: usage.cacheWrite,
+        tokens_total: usage.totalTokens,
+        cost_usd: usage.cost.total,
         model: modelId,
     };
     logger.projectComplete(stats);
@@ -300,7 +302,6 @@ async function main() {
 }
 main().catch((err) => {
     releaseLock(getBaseDir());
-    // Last-resort logging - config may not have loaded
     const logger = new AnalyzeLogger();
     logger.error("Fatal error", err);
     process.exit(1);