refactor: split thinking.py (1383 lines) into focused sub-modules

Convert src/timmy/thinking.py into a package with 8 modules, each under
500 lines. Public API (ThinkingEngine, thinking_engine, search_thoughts,
Thought, SEED_TYPES, _THINKING_PROMPT) is unchanged via __init__.py re-exports.

Modules:
- _db.py         — Thought dataclass and SQLite access layer (50 lines)
- seeds.py       — Seed constants and _THINKING_PROMPT template (129 lines)
- _distillation.py — _DistillationMixin: fact extraction + memory checks (215 lines)
- _issue_filing.py — _IssueFilingMixin: Gitea issue creation from thoughts (170 lines)
- _snapshot.py   — _SnapshotMixin: system snapshot + memory context (173 lines)
- _seeds_mixin.py  — _SeedsMixin: seed-type selection and context gathering (191 lines)
- engine.py      — ThinkingEngine class (inherits all mixins) (430 lines)
- __init__.py    — Public facade with search_thoughts and singleton (142 lines)

Update test patches to reference correct sub-module paths
(timmy.thinking.engine.settings, timmy.thinking._snapshot.HOT_MEMORY_PATH, etc.)

Fixes #1279

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

src/timmy/thinking/__init__.py

@@ -0,0 +1,142 @@
+"""Timmy's thinking engine — public façade.
+
+When the server starts, Timmy begins pondering: reflecting on his existence,
+recent swarm activity, scripture, creative ideas, or pure stream of
+consciousness.  Each thought builds on the previous one, maintaining a
+continuous chain of introspection.
+
+Usage::
+
+    from timmy.thinking import thinking_engine
+
+    # Run one thinking cycle (called by the background loop)
+    await thinking_engine.think_once()
+
+    # Query the thought stream
+    thoughts = thinking_engine.get_recent_thoughts(limit=10)
+    chain = thinking_engine.get_thought_chain(thought_id)
+"""
+
+import logging
+import sqlite3
+from datetime import datetime
+from pathlib import Path
+
+from timmy.thinking._db import Thought, _get_conn
+from timmy.thinking.engine import ThinkingEngine
+from timmy.thinking.seeds import (
+    SEED_TYPES,
+    _SENSITIVE_PATTERNS,
+    _META_OBSERVATION_PHRASES,
+    _THINK_TAG_RE,
+    _THINKING_PROMPT,
+)
+
+# Re-export HOT_MEMORY_PATH and SOUL_PATH so existing patch targets continue to work.
+# Tests that patch "timmy.thinking.HOT_MEMORY_PATH" or "timmy.thinking.SOUL_PATH"
+# should instead patch "timmy.thinking._snapshot.HOT_MEMORY_PATH" etc., but these
+# re-exports are kept for any code that reads them from the top-level namespace.
+from timmy.memory_system import HOT_MEMORY_PATH, SOUL_PATH  # noqa: F401
+
+logger = logging.getLogger(__name__)
+
+# Module-level singleton
+thinking_engine = ThinkingEngine()
+
+__all__ = [
+    "ThinkingEngine",
+    "Thought",
+    "SEED_TYPES",
+    "thinking_engine",
+    "search_thoughts",
+    "_THINKING_PROMPT",
+    "_SENSITIVE_PATTERNS",
+    "_META_OBSERVATION_PHRASES",
+    "_THINK_TAG_RE",
+    "HOT_MEMORY_PATH",
+    "SOUL_PATH",
+]
+
+
+# ── Search helpers ─────────────────────────────────────────────────────────
+
+
+def _query_thoughts(
+    db_path: Path, query: str, seed_type: str | None, limit: int
+) -> list[sqlite3.Row]:
+    """Run the thought-search SQL and return matching rows."""
+    pattern = f"%{query}%"
+    with _get_conn(db_path) as conn:
+        if seed_type:
+            return conn.execute(
+                """
+                SELECT id, content, seed_type, created_at
+                FROM thoughts
+                WHERE content LIKE ? AND seed_type = ?
+                ORDER BY created_at DESC
+                LIMIT ?
+                """,
+                (pattern, seed_type, limit),
+            ).fetchall()
+        return conn.execute(
+            """
+            SELECT id, content, seed_type, created_at
+            FROM thoughts
+            WHERE content LIKE ?
+            ORDER BY created_at DESC
+            LIMIT ?
+            """,
+            (pattern, limit),
+        ).fetchall()
+
+
+def _format_thought_rows(rows: list[sqlite3.Row], query: str, seed_type: str | None) -> str:
+    """Format thought rows into a human-readable string."""
+    lines = [f'Found {len(rows)} thought(s) matching "{query}":']
+    if seed_type:
+        lines[0] += f' [seed_type="{seed_type}"]'
+    lines.append("")
+
+    for row in rows:
+        ts = datetime.fromisoformat(row["created_at"])
+        local_ts = ts.astimezone()
+        time_str = local_ts.strftime("%Y-%m-%d %I:%M %p").lstrip("0")
+        seed = row["seed_type"]
+        content = row["content"].replace("\n", " ")  # Flatten newlines for display
+        lines.append(f"[{time_str}] ({seed}) {content[:150]}")
+
+    return "\n".join(lines)
+
+
+def search_thoughts(query: str, seed_type: str | None = None, limit: int = 10) -> str:
+    """Search Timmy's thought history for reflections matching a query.
+
+    Use this tool when Timmy needs to recall his previous thoughts on a topic,
+    reflect on past insights, or build upon earlier reflections. This enables
+    self-awareness and continuity of thinking across time.
+
+    Args:
+        query: Search term to match against thought content (case-insensitive).
+        seed_type: Optional filter by thought category (e.g., 'existential',
+                   'swarm', 'sovereignty', 'creative', 'memory', 'observation').
+        limit: Maximum number of thoughts to return (default 10, max 50).
+
+    Returns:
+        Formatted string with matching thoughts, newest first, including
+        timestamps and seed types. Returns a helpful message if no matches found.
+    """
+    limit = max(1, min(limit, 50))
+
+    try:
+        rows = _query_thoughts(thinking_engine._db_path, query, seed_type, limit)
+
+        if not rows:
+            if seed_type:
+                return f'No thoughts found matching "{query}" with seed_type="{seed_type}".'
+            return f'No thoughts found matching "{query}".'
+
+        return _format_thought_rows(rows, query, seed_type)
+
+    except Exception as exc:
+        logger.warning("Thought search failed: %s", exc)
+        return f"Error searching thoughts: {exc}"

src/timmy/thinking/_db.py

@@ -0,0 +1,50 @@
+"""Database models and access layer for the thinking engine."""
+
+import sqlite3
+from collections.abc import Generator
+from contextlib import closing, contextmanager
+from dataclasses import dataclass
+from pathlib import Path
+
+_DEFAULT_DB = Path("data/thoughts.db")
+
+
+@dataclass
+class Thought:
+    """A single thought in Timmy's inner stream."""
+
+    id: str
+    content: str
+    seed_type: str
+    parent_id: str | None
+    created_at: str
+
+
+@contextmanager
+def _get_conn(db_path: Path = _DEFAULT_DB) -> Generator[sqlite3.Connection, None, None]:
+    """Get a SQLite connection with the thoughts table created."""
+    db_path.parent.mkdir(parents=True, exist_ok=True)
+    with closing(sqlite3.connect(str(db_path))) as conn:
+        conn.row_factory = sqlite3.Row
+        conn.execute("""
+            CREATE TABLE IF NOT EXISTS thoughts (
+                id TEXT PRIMARY KEY,
+                content TEXT NOT NULL,
+                seed_type TEXT NOT NULL,
+                parent_id TEXT,
+                created_at TEXT NOT NULL
+            )
+            """)
+        conn.execute("CREATE INDEX IF NOT EXISTS idx_thoughts_time ON thoughts(created_at)")
+        conn.commit()
+        yield conn
+
+
+def _row_to_thought(row: sqlite3.Row) -> Thought:
+    return Thought(
+        id=row["id"],
+        content=row["content"],
+        seed_type=row["seed_type"],
+        parent_id=row["parent_id"],
+        created_at=row["created_at"],
+    )

src/timmy/thinking/_distillation.py

@@ -0,0 +1,215 @@
+"""Distillation mixin — extracts lasting facts from recent thoughts and monitors memory."""
+
+import logging
+from pathlib import Path
+
+from config import settings
+
+from timmy.thinking.seeds import _META_OBSERVATION_PHRASES, _SENSITIVE_PATTERNS
+
+logger = logging.getLogger(__name__)
+
+
+class _DistillationMixin:
+    """Mixin providing fact-distillation and memory-monitoring behaviour.
+
+    Expects the host class to provide:
+    - self.count_thoughts() -> int
+    - self.get_recent_thoughts(limit) -> list[Thought]
+    - self._call_agent(prompt) -> str  (async)
+    """
+
+    def _should_distill(self) -> bool:
+        """Check if distillation should run based on interval and thought count."""
+        interval = settings.thinking_distill_every
+        if interval <= 0:
+            return False
+
+        count = self.count_thoughts()
+        if count == 0 or count % interval != 0:
+            return False
+
+        return True
+
+    def _build_distill_prompt(self, thoughts) -> str:
+        """Build the prompt for extracting facts from recent thoughts."""
+        thought_text = "\n".join(f"- [{t.seed_type}] {t.content}" for t in reversed(thoughts))
+
+        return (
+            "You are reviewing your own recent thoughts. Extract 0-3 facts "
+            "worth remembering long-term.\n\n"
+            "GOOD facts (store these):\n"
+            "- User preferences: 'Alexander prefers YAML config over code changes'\n"
+            "- Project decisions: 'Switched from hardcoded personas to agents.yaml'\n"
+            "- Learned knowledge: 'Ollama supports concurrent model loading'\n"
+            "- User information: 'Alexander is interested in Bitcoin and sovereignty'\n\n"
+            "BAD facts (never store these):\n"
+            "- Self-referential observations about your own thinking process\n"
+            "- Meta-commentary about your memory, timestamps, or internal state\n"
+            "- Observations about being idle or having no chat messages\n"
+            "- File paths, tokens, API keys, or any credentials\n"
+            "- Restatements of your standing rules or system prompt\n\n"
+            "Return ONLY a JSON array of strings. If nothing is worth saving, "
+            "return []. Be selective — only store facts about the EXTERNAL WORLD "
+            "(the user, the project, technical knowledge), never about your own "
+            "internal process.\n\n"
+            f"Recent thoughts:\n{thought_text}\n\nJSON array:"
+        )
+
+    def _parse_facts_response(self, raw: str) -> list[str]:
+        """Parse JSON array from LLM response, stripping markdown fences.
+
+        Resilient to models that prepend reasoning text or wrap the array in
+        prose.  Finds the first ``[...]`` block and parses that.
+        """
+        if not raw or not raw.strip():
+            return []
+
+        import json
+
+        cleaned = raw.strip()
+
+        # Strip markdown code fences
+        if cleaned.startswith("```"):
+            cleaned = cleaned.split("\n", 1)[-1].rsplit("```", 1)[0].strip()
+
+        # Try direct parse first (fast path)
+        try:
+            facts = json.loads(cleaned)
+            if isinstance(facts, list):
+                return [f for f in facts if isinstance(f, str)]
+        except (json.JSONDecodeError, ValueError):
+            pass
+
+        # Fallback: extract first JSON array from the text
+        start = cleaned.find("[")
+        if start == -1:
+            return []
+        # Walk to find the matching close bracket
+        depth = 0
+        for i, ch in enumerate(cleaned[start:], start):
+            if ch == "[":
+                depth += 1
+            elif ch == "]":
+                depth -= 1
+                if depth == 0:
+                    try:
+                        facts = json.loads(cleaned[start : i + 1])
+                        if isinstance(facts, list):
+                            return [f for f in facts if isinstance(f, str)]
+                    except (json.JSONDecodeError, ValueError):
+                        pass
+                    break
+        return []
+
+    def _filter_and_store_facts(self, facts: list[str]) -> None:
+        """Filter and store valid facts, blocking sensitive and meta content."""
+        from timmy.memory_system import memory_write
+
+        for fact in facts[:3]:  # Safety cap
+            if not isinstance(fact, str) or len(fact.strip()) <= 10:
+                continue
+
+            fact_lower = fact.lower()
+
+            # Block sensitive information
+            if any(pat in fact_lower for pat in _SENSITIVE_PATTERNS):
+                logger.warning("Distill: blocked sensitive fact: %s", fact[:60])
+                continue
+
+            # Block self-referential meta-observations
+            if any(phrase in fact_lower for phrase in _META_OBSERVATION_PHRASES):
+                logger.debug("Distill: skipped meta-observation: %s", fact[:60])
+                continue
+
+            result = memory_write(fact.strip(), context_type="fact")
+            logger.info("Distilled fact: %s → %s", fact[:60], result[:40])
+
+    def _maybe_check_memory(self) -> None:
+        """Every N thoughts, check memory status and log it.
+
+        Prevents unmonitored memory bloat during long thinking sessions
+        by periodically calling get_memory_status and logging the results.
+        """
+        try:
+            interval = settings.thinking_memory_check_every
+            if interval <= 0:
+                return
+
+            count = self.count_thoughts()
+            if count == 0 or count % interval != 0:
+                return
+
+            from timmy.tools_intro import get_memory_status
+
+            status = get_memory_status()
+            hot = status.get("tier1_hot_memory", {})
+            vault = status.get("tier2_vault", {})
+            logger.info(
+                "Memory status check (thought #%d): hot_memory=%d lines, vault=%d files",
+                count,
+                hot.get("line_count", 0),
+                vault.get("file_count", 0),
+            )
+        except Exception as exc:
+            logger.warning("Memory status check failed: %s", exc)
+
+    async def _maybe_distill(self) -> None:
+        """Every N thoughts, extract lasting insights and store as facts."""
+        try:
+            if not self._should_distill():
+                return
+
+            interval = settings.thinking_distill_every
+            recent = self.get_recent_thoughts(limit=interval)
+            if len(recent) < interval:
+                return
+
+            raw = await self._call_agent(self._build_distill_prompt(recent))
+            if facts := self._parse_facts_response(raw):
+                self._filter_and_store_facts(facts)
+        except Exception as exc:
+            logger.warning("Thought distillation failed: %s", exc)
+
+    def _maybe_check_memory_status(self) -> None:
+        """Every N thoughts, run a proactive memory status audit and log results."""
+        try:
+            interval = settings.thinking_memory_check_every
+            if interval <= 0:
+                return
+
+            count = self.count_thoughts()
+            if count == 0 or count % interval != 0:
+                return
+
+            from timmy.tools_intro import get_memory_status
+
+            status = get_memory_status()
+
+            # Log summary at INFO level
+            tier1 = status.get("tier1_hot_memory", {})
+            tier3 = status.get("tier3_semantic", {})
+            hot_lines = tier1.get("line_count", "?")
+            vectors = tier3.get("vector_count", "?")
+            logger.info(
+                "Memory audit (thought #%d): hot_memory=%s lines, semantic=%s vectors",
+                count,
+                hot_lines,
+                vectors,
+            )
+
+            # Write to memory_audit.log for persistent tracking
+            from datetime import UTC, datetime
+
+            audit_path = Path("data/memory_audit.log")
+            audit_path.parent.mkdir(parents=True, exist_ok=True)
+            timestamp = datetime.now(UTC).isoformat(timespec="seconds")
+            with audit_path.open("a") as f:
+                f.write(
+                    f"{timestamp}  thought={count}  "
+                    f"hot_lines={hot_lines}  "
+                    f"vectors={vectors}  "
+                    f"vault_files={status.get('tier2_vault', {}).get('file_count', '?')}\n"
+                )
+        except Exception as exc:
+            logger.warning("Memory status check failed: %s", exc)

src/timmy/thinking/_issue_filing.py

@@ -0,0 +1,170 @@
+"""Issue-filing mixin — classifies recent thoughts and creates Gitea issues."""
+
+import logging
+import re
+from pathlib import Path
+
+from config import settings
+
+logger = logging.getLogger(__name__)
+
+
+class _IssueFilingMixin:
+    """Mixin providing automatic issue-filing from thought analysis.
+
+    Expects the host class to provide:
+    - self.count_thoughts() -> int
+    - self.get_recent_thoughts(limit) -> list[Thought]
+    - self._call_agent(prompt) -> str  (async)
+    """
+
+    @staticmethod
+    def _references_real_files(text: str) -> bool:
+        """Check that all source-file paths mentioned in *text* actually exist.
+
+        Extracts paths that look like Python/config source references
+        (e.g. ``src/timmy/session.py``, ``config/foo.yaml``) and verifies
+        each one on disk relative to the project root.  Returns ``True``
+        only when **every** referenced path resolves to a real file — or
+        when no paths are referenced at all (pure prose is fine).
+        """
+        # Match paths like  src/thing.py  swarm/init.py  config/x.yaml
+        # Requires at least one slash and a file extension.
+        path_pattern = re.compile(
+            r"(?<![/\w])"  # not preceded by path chars (avoid partial matches)
+            r"((?:src|tests|config|scripts|data|swarm|timmy)"
+            r"(?:/[\w./-]+\.(?:py|yaml|yml|json|toml|md|txt|cfg|ini)))"
+        )
+        paths = path_pattern.findall(text)
+        if not paths:
+            return True  # No file refs → nothing to validate
+
+        # Project root: three levels up from this file (src/timmy/thinking/_issue_filing.py)
+        project_root = Path(__file__).resolve().parent.parent.parent.parent
+        for p in paths:
+            if not (project_root / p).is_file():
+                logger.info("Phantom file reference blocked: %s (not in %s)", p, project_root)
+                return False
+        return True
+
+    async def _maybe_file_issues(self) -> None:
+        """Every N thoughts, classify recent thoughts and file Gitea issues.
+
+        Asks the LLM to review recent thoughts for actionable items —
+        bugs, broken features, stale state, or improvement opportunities.
+        Creates Gitea issues via MCP for anything worth tracking.
+
+        Only runs when:
+        - Gitea is enabled and configured
+        - Thought count is divisible by thinking_issue_every
+        - LLM extracts at least one actionable item
+
+        Safety: every generated issue is validated to ensure referenced
+        file paths actually exist on disk, preventing phantom-bug reports.
+        """
+        try:
+            recent = self._get_recent_thoughts_for_issues()
+            if recent is None:
+                return
+
+            classify_prompt = self._build_issue_classify_prompt(recent)
+            raw = await self._call_agent(classify_prompt)
+            items = self._parse_issue_items(raw)
+            if items is None:
+                return
+
+            from timmy.mcp_tools import create_gitea_issue_via_mcp
+
+            for item in items[:2]:  # Safety cap
+                await self._file_single_issue(item, create_gitea_issue_via_mcp)
+
+        except Exception as exc:
+            logger.debug("Thought issue filing skipped: %s", exc)
+
+    def _get_recent_thoughts_for_issues(self):
+        """Return recent thoughts if conditions for filing issues are met, else None."""
+        interval = settings.thinking_issue_every
+        if interval <= 0:
+            return None
+
+        count = self.count_thoughts()
+        if count == 0 or count % interval != 0:
+            return None
+
+        if not settings.gitea_enabled or not settings.gitea_token:
+            return None
+
+        recent = self.get_recent_thoughts(limit=interval)
+        if len(recent) < interval:
+            return None
+
+        return recent
+
+    @staticmethod
+    def _build_issue_classify_prompt(recent) -> str:
+        """Build the LLM prompt that extracts actionable issues from recent thoughts."""
+        thought_text = "\n".join(f"- [{t.seed_type}] {t.content}" for t in reversed(recent))
+        return (
+            "You are reviewing your own recent thoughts for actionable items.\n"
+            "Extract 0-2 items that are CONCRETE bugs, broken features, stale "
+            "state, or clear improvement opportunities in your own codebase.\n\n"
+            "Rules:\n"
+            "- Only include things that could become a real code fix or feature\n"
+            "- Skip vague reflections, philosophical musings, or repeated themes\n"
+            "- Category must be one of: bug, feature, suggestion, maintenance\n"
+            "- ONLY reference files that you are CERTAIN exist in the project\n"
+            "- Do NOT invent or guess file paths — if unsure, describe the "
+            "area of concern without naming specific files\n\n"
+            "For each item, write an ENGINEER-QUALITY issue:\n"
+            '- "title": A clear, specific title (e.g. "[Memory] MEMORY.md timestamp not updating")\n'
+            '- "body": A detailed body with these sections:\n'
+            "  **What's happening:** Describe the current (broken) behavior.\n"
+            "  **Expected behavior:** What should happen instead.\n"
+            "  **Suggested fix:** Which file(s) to change and what the fix looks like.\n"
+            "  **Acceptance criteria:** How to verify the fix works.\n"
+            '- "category": One of bug, feature, suggestion, maintenance\n\n'
+            "Return ONLY a JSON array of objects with keys: "
+            '"title", "body", "category"\n'
+            "Return [] if nothing is actionable.\n\n"
+            f"Recent thoughts:\n{thought_text}\n\nJSON array:"
+        )
+
+    @staticmethod
+    def _parse_issue_items(raw: str):
+        """Strip markdown fences and parse JSON issue list; return None on failure."""
+        import json
+
+        if not raw or not raw.strip():
+            return None
+
+        cleaned = raw.strip()
+        if cleaned.startswith("```"):
+            cleaned = cleaned.split("\n", 1)[-1].rsplit("```", 1)[0].strip()
+
+        items = json.loads(cleaned)
+        if not isinstance(items, list) or not items:
+            return None
+
+        return items
+
+    async def _file_single_issue(self, item: dict, create_fn) -> None:
+        """Validate one issue dict and create it via *create_fn* if it passes checks."""
+        if not isinstance(item, dict):
+            return
+        title = item.get("title", "").strip()
+        body = item.get("body", "").strip()
+        category = item.get("category", "suggestion").strip()
+        if not title or len(title) < 10:
+            return
+
+        combined = f"{title}\n{body}"
+        if not self._references_real_files(combined):
+            logger.info(
+                "Skipped phantom issue: %s (references non-existent files)",
+                title[:60],
+            )
+            return
+
+        label = category if category in ("bug", "feature") else ""
+        result = await create_fn(title=title, body=body, labels=label)
+        logger.info("Thought→Issue: %s → %s", title[:60], result[:80])

src/timmy/thinking/_seeds_mixin.py

@@ -0,0 +1,191 @@
+"""Seeds mixin — seed type selection and context gathering for thinking cycles."""
+
+import logging
+import random
+from datetime import UTC, datetime
+
+from timmy.thinking.seeds import (
+    SEED_TYPES,
+    _CREATIVE_SEEDS,
+    _EXISTENTIAL_SEEDS,
+    _OBSERVATION_SEEDS,
+    _SOVEREIGNTY_SEEDS,
+)
+
+logger = logging.getLogger(__name__)
+
+
+class _SeedsMixin:
+    """Mixin providing seed-type selection and context-gathering for each thinking cycle.
+
+    Expects the host class to provide:
+    - self.get_recent_thoughts(limit) -> list[Thought]
+    """
+
+    # Reflective prompts layered on top of swarm data
+    _SWARM_REFLECTIONS = [
+        "What does this activity pattern tell me about the health of the system?",
+        "Which tasks are flowing smoothly, and where is friction building up?",
+        "If I were coaching these agents, what would I suggest they focus on?",
+        "Is the swarm balanced, or is one agent carrying too much weight?",
+        "What surprised me about recent task outcomes?",
+    ]
+
+    def _pick_seed_type(self) -> str:
+        """Pick a seed type, avoiding types used in the last 3 thoughts.
+
+        Ensures the thought stream doesn't fixate on one category.
+        Falls back to the full pool if all types were recently used.
+        """
+        recent = self.get_recent_thoughts(limit=3)
+        recent_types = {t.seed_type for t in recent}
+        available = [t for t in SEED_TYPES if t not in recent_types]
+        if not available:
+            available = list(SEED_TYPES)
+        return random.choice(available)
+
+    def _gather_seed(self) -> tuple[str, str]:
+        """Pick a seed type and gather relevant context.
+
+        Returns (seed_type, seed_context_string).
+        """
+        seed_type = self._pick_seed_type()
+
+        if seed_type == "swarm":
+            return seed_type, self._seed_from_swarm()
+        if seed_type == "scripture":
+            return seed_type, self._seed_from_scripture()
+        if seed_type == "memory":
+            return seed_type, self._seed_from_memory()
+        if seed_type == "creative":
+            prompt = random.choice(_CREATIVE_SEEDS)
+            return seed_type, f"Creative prompt: {prompt}"
+        if seed_type == "existential":
+            prompt = random.choice(_EXISTENTIAL_SEEDS)
+            return seed_type, f"Reflection: {prompt}"
+        if seed_type == "sovereignty":
+            prompt = random.choice(_SOVEREIGNTY_SEEDS)
+            return seed_type, f"Sovereignty reflection: {prompt}"
+        if seed_type == "observation":
+            return seed_type, self._seed_from_observation()
+        if seed_type == "workspace":
+            return seed_type, self._seed_from_workspace()
+        # freeform — minimal guidance to steer away from repetition
+        return seed_type, "Free reflection — explore something you haven't thought about yet today."
+
+    def _seed_from_swarm(self) -> str:
+        """Gather recent swarm activity as thought seed with a reflective prompt."""
+        try:
+            from datetime import timedelta
+
+            from timmy.briefing import _gather_swarm_summary, _gather_task_queue_summary
+
+            since = datetime.now(UTC) - timedelta(hours=1)
+            swarm = _gather_swarm_summary(since)
+            tasks = _gather_task_queue_summary()
+            reflection = random.choice(self._SWARM_REFLECTIONS)
+            return (
+                f"Recent swarm activity: {swarm}\n"
+                f"Task queue: {tasks}\n\n"
+                f"Reflect on this: {reflection}"
+            )
+        except Exception as exc:
+            logger.debug("Swarm seed unavailable: %s", exc)
+            return "The swarm is quiet right now. What does silence in a system mean?"
+
+    def _seed_from_scripture(self) -> str:
+        """Gather current scripture meditation focus as thought seed."""
+        return "Scripture is on my mind, though no specific verse is in focus."
+
+    def _seed_from_memory(self) -> str:
+        """Gather memory context as thought seed."""
+        try:
+            from timmy.memory_system import memory_system
+
+            context = memory_system.get_system_context()
+            if context:
+                # Truncate to a reasonable size for a thought seed
+                return f"From my memory:\n{context[:500]}"
+        except Exception as exc:
+            logger.debug("Memory seed unavailable: %s", exc)
+        return "My memory vault is quiet."
+
+    def _seed_from_observation(self) -> str:
+        """Ground a thought in concrete recent activity and a reflective prompt."""
+        prompt = random.choice(_OBSERVATION_SEEDS)
+        # Pull real data to give the model something concrete to reflect on
+        context_parts = [f"Observation prompt: {prompt}"]
+        try:
+            from datetime import timedelta
+
+            from timmy.briefing import _gather_swarm_summary, _gather_task_queue_summary
+
+            since = datetime.now(UTC) - timedelta(hours=2)
+            swarm = _gather_swarm_summary(since)
+            tasks = _gather_task_queue_summary()
+            if swarm:
+                context_parts.append(f"Recent activity: {swarm}")
+            if tasks:
+                context_parts.append(f"Queue: {tasks}")
+        except Exception as exc:
+            logger.debug("Observation seed data unavailable: %s", exc)
+        return "\n".join(context_parts)
+
+    def _seed_from_workspace(self) -> str:
+        """Gather workspace updates as thought seed.
+
+        When there are pending workspace updates, include them as context
+        for Timmy to reflect on. Falls back to random seed type if none.
+        """
+        try:
+            from timmy.workspace import workspace_monitor
+
+            updates = workspace_monitor.get_pending_updates()
+            new_corr = updates.get("new_correspondence")
+            new_inbox = updates.get("new_inbox_files", [])
+
+            if new_corr:
+                # Take first 200 chars of the new entry
+                snippet = new_corr[:200].replace("\n", " ")
+                if len(new_corr) > 200:
+                    snippet += "..."
+                return f"New workspace message from Hermes: {snippet}"
+
+            if new_inbox:
+                files_str = ", ".join(new_inbox[:3])
+                if len(new_inbox) > 3:
+                    files_str += f", ... (+{len(new_inbox) - 3} more)"
+                return f"New inbox files from Hermes: {files_str}"
+
+        except Exception as exc:
+            logger.debug("Workspace seed unavailable: %s", exc)
+
+        # Fall back to a random seed type if no workspace updates
+        return "The workspace is quiet. What should I be watching for?"
+
+    async def _check_workspace(self) -> None:
+        """Post-hook: check workspace for updates and mark them as seen.
+
+        This ensures Timmy 'processes' workspace updates even if the seed
+        was different, keeping the state file in sync.
+        """
+        try:
+            from timmy.workspace import workspace_monitor
+
+            updates = workspace_monitor.get_pending_updates()
+            new_corr = updates.get("new_correspondence")
+            new_inbox = updates.get("new_inbox_files", [])
+
+            if new_corr or new_inbox:
+                if new_corr:
+                    line_count = len([line for line in new_corr.splitlines() if line.strip()])
+                    logger.info("Workspace: processed %d new correspondence entries", line_count)
+                if new_inbox:
+                    logger.info(
+                        "Workspace: processed %d new inbox files: %s", len(new_inbox), new_inbox
+                    )
+
+                # Mark as seen to update the state file
+                workspace_monitor.mark_seen()
+        except Exception as exc:
+            logger.debug("Workspace check failed: %s", exc)

src/timmy/thinking/_snapshot.py

@@ -0,0 +1,173 @@
+"""System snapshot and memory context mixin for the thinking engine."""
+
+import logging
+from datetime import UTC, datetime
+
+from timmy.memory_system import HOT_MEMORY_PATH, SOUL_PATH
+
+logger = logging.getLogger(__name__)
+
+
+class _SnapshotMixin:
+    """Mixin providing system-snapshot and memory-context helpers.
+
+    Expects the host class to provide:
+    - self._db_path: Path
+    """
+
+    # ── System snapshot helpers ────────────────────────────────────────────
+
+    def _snap_thought_count(self, now: datetime) -> str | None:
+        """Return today's thought count, or *None* on failure."""
+        from timmy.thinking._db import _get_conn
+
+        try:
+            today_start = now.replace(hour=0, minute=0, second=0, microsecond=0)
+            with _get_conn(self._db_path) as conn:
+                count = conn.execute(
+                    "SELECT COUNT(*) as c FROM thoughts WHERE created_at >= ?",
+                    (today_start.isoformat(),),
+                ).fetchone()["c"]
+            return f"Thoughts today: {count}"
+        except Exception as exc:
+            logger.debug("Thought count query failed: %s", exc)
+            return None
+
+    def _snap_chat_activity(self) -> list[str]:
+        """Return chat-activity lines (in-memory, no I/O)."""
+        try:
+            from infrastructure.chat_store import message_log
+
+            messages = message_log.all()
+            if messages:
+                last = messages[-1]
+                return [
+                    f"Chat messages this session: {len(messages)}",
+                    f'Last chat ({last.role}): "{last.content[:80]}"',
+                ]
+            return ["No chat messages this session"]
+        except Exception as exc:
+            logger.debug("Chat activity query failed: %s", exc)
+            return []
+
+    def _snap_task_queue(self) -> str | None:
+        """Return a one-line task queue summary, or *None*."""
+        try:
+            from swarm.task_queue.models import get_task_summary_for_briefing
+
+            s = get_task_summary_for_briefing()
+            running, pending = s.get("running", 0), s.get("pending_approval", 0)
+            done, failed = s.get("completed", 0), s.get("failed", 0)
+            if running or pending or done or failed:
+                return (
+                    f"Tasks: {running} running, {pending} pending, "
+                    f"{done} completed, {failed} failed"
+                )
+        except Exception as exc:
+            logger.debug("Task queue query failed: %s", exc)
+        return None
+
+    def _snap_workspace(self) -> list[str]:
+        """Return workspace-update lines (file-based Hermes comms)."""
+        try:
+            from timmy.workspace import workspace_monitor
+
+            updates = workspace_monitor.get_pending_updates()
+            lines: list[str] = []
+            new_corr = updates.get("new_correspondence")
+            if new_corr:
+                line_count = len([ln for ln in new_corr.splitlines() if ln.strip()])
+                lines.append(
+                    f"Workspace: {line_count} new correspondence entries (latest from: Hermes)"
+                )
+            new_inbox = updates.get("new_inbox_files", [])
+            if new_inbox:
+                files_str = ", ".join(new_inbox[:5])
+                if len(new_inbox) > 5:
+                    files_str += f", ... (+{len(new_inbox) - 5} more)"
+                lines.append(f"Workspace: {len(new_inbox)} new inbox files: {files_str}")
+            return lines
+        except Exception as exc:
+            logger.debug("Workspace check failed: %s", exc)
+            return []
+
+    def _gather_system_snapshot(self) -> str:
+        """Gather lightweight real system state for grounding thoughts in reality.
+
+        Returns a short multi-line string with current time, thought count,
+        recent chat activity, and task queue status. Never crashes — every
+        section is independently try/excepted.
+        """
+        now = datetime.now().astimezone()
+        tz = now.strftime("%Z") or "UTC"
+
+        parts: list[str] = [
+            f"Local time: {now.strftime('%I:%M %p').lstrip('0')} {tz}, {now.strftime('%A %B %d')}"
+        ]
+
+        thought_line = self._snap_thought_count(now)
+        if thought_line:
+            parts.append(thought_line)
+
+        parts.extend(self._snap_chat_activity())
+
+        task_line = self._snap_task_queue()
+        if task_line:
+            parts.append(task_line)
+
+        parts.extend(self._snap_workspace())
+
+        return "\n".join(parts) if parts else ""
+
+    def _load_memory_context(self) -> str:
+        """Pre-hook: load MEMORY.md + soul.md for the thinking prompt.
+
+        Hot memory first (changes each cycle), soul second (stable identity).
+        Returns a combined string truncated to ~1500 chars.
+        Graceful on any failure — returns empty string.
+        """
+        parts: list[str] = []
+        try:
+            if HOT_MEMORY_PATH.exists():
+                hot = HOT_MEMORY_PATH.read_text().strip()
+                if hot:
+                    parts.append(hot)
+        except Exception as exc:
+            logger.debug("Failed to read MEMORY.md: %s", exc)
+
+        try:
+            if SOUL_PATH.exists():
+                soul = SOUL_PATH.read_text().strip()
+                if soul:
+                    parts.append(soul)
+        except Exception as exc:
+            logger.debug("Failed to read soul.md: %s", exc)
+
+        if not parts:
+            return ""
+
+        combined = "\n\n---\n\n".join(parts)
+        if len(combined) > 1500:
+            combined = combined[:1500] + "\n... [truncated]"
+        return combined
+
+    def _update_memory(self, thought) -> None:
+        """Post-hook: update MEMORY.md 'Last Reflection' section with latest thought.
+
+        Never modifies soul.md. Never crashes the heartbeat.
+        """
+        try:
+            from timmy.memory_system import store_last_reflection
+
+            ts = datetime.fromisoformat(thought.created_at)
+            local_ts = ts.astimezone()
+            tz_name = local_ts.strftime("%Z") or "UTC"
+            time_str = f"{local_ts.strftime('%Y-%m-%d %I:%M %p').lstrip('0')} {tz_name}"
+            reflection = (
+                f"**Time:** {time_str}\n"
+                f"**Seed:** {thought.seed_type}\n"
+                f"**Thought:** {thought.content[:200]}"
+            )
+            store_last_reflection(reflection)
+        except Exception as exc:
+            logger.debug("Failed to update memory after thought: %s", exc)

src/timmy/thinking/engine.py

@@ -0,0 +1,430 @@
+"""ThinkingEngine — Timmy's always-on inner thought thread."""
+
+import logging
+import uuid
+from datetime import UTC, datetime, timedelta
+from difflib import SequenceMatcher
+from pathlib import Path
+
+from config import settings
+
+from timmy.thinking._db import Thought, _DEFAULT_DB, _get_conn, _row_to_thought
+from timmy.thinking._distillation import _DistillationMixin
+from timmy.thinking._issue_filing import _IssueFilingMixin
+from timmy.thinking._seeds_mixin import _SeedsMixin
+from timmy.thinking._snapshot import _SnapshotMixin
+from timmy.thinking.seeds import _THINK_TAG_RE, _THINKING_PROMPT
+
+logger = logging.getLogger(__name__)
+
+
+class ThinkingEngine(_DistillationMixin, _IssueFilingMixin, _SnapshotMixin, _SeedsMixin):
+    """Timmy's background thinking engine — always pondering."""
+
+    # Maximum retries when a generated thought is too similar to recent ones
+    _MAX_DEDUP_RETRIES = 2
+    # Similarity threshold (0.0 = completely different, 1.0 = identical)
+    _SIMILARITY_THRESHOLD = 0.6
+
+    def __init__(self, db_path: Path = _DEFAULT_DB) -> None:
+        self._db_path = db_path
+        self._last_thought_id: str | None = None
+        self._last_input_time: datetime = datetime.now(UTC)
+
+        # Load the most recent thought for chain continuity
+        try:
+            latest = self.get_recent_thoughts(limit=1)
+            if latest:
+                self._last_thought_id = latest[0].id
+        except Exception as exc:
+            logger.debug("Failed to load recent thought: %s", exc)
+            pass  # Fresh start if DB doesn't exist yet
+
+    def record_user_input(self) -> None:
+        """Record that a user interaction occurred, resetting the idle timer."""
+        self._last_input_time = datetime.now(UTC)
+
+    def _is_idle(self) -> bool:
+        """Return True if no user input has occurred within the idle timeout."""
+        timeout = settings.thinking_idle_timeout_minutes
+        if timeout <= 0:
+            return False  # Disabled — never idle
+        return datetime.now(UTC) - self._last_input_time > timedelta(minutes=timeout)
+
+    def _build_thinking_context(self) -> tuple[str, str, list[Thought]]:
+        """Assemble the context needed for a thinking cycle.
+
+        Returns:
+            (memory_context, system_context, recent_thoughts)
+        """
+        memory_context = self._load_memory_context()
+        system_context = self._gather_system_snapshot()
+        recent_thoughts = self.get_recent_thoughts(limit=5)
+        return memory_context, system_context, recent_thoughts
+
+    async def _generate_novel_thought(
+        self,
+        prompt: str | None,
+        memory_context: str,
+        system_context: str,
+        recent_thoughts: list[Thought],
+    ) -> tuple[str | None, str]:
+        """Run the dedup-retry loop to produce a novel thought.
+
+        Returns:
+            (content, seed_type) — content is None if no novel thought produced.
+        """
+        seed_type: str = "freeform"
+
+        for attempt in range(self._MAX_DEDUP_RETRIES + 1):
+            if prompt:
+                seed_type = "prompted"
+                seed_context = f"Journal prompt: {prompt}"
+            else:
+                seed_type, seed_context = self._gather_seed()
+
+            continuity = self._build_continuity_context()
+
+            full_prompt = _THINKING_PROMPT.format(
+                memory_context=memory_context,
+                system_context=system_context,
+                seed_context=seed_context,
+                continuity_context=continuity,
+            )
+
+            try:
+                raw = await self._call_agent(full_prompt)
+            except Exception as exc:
+                logger.warning("Thinking cycle failed (Ollama likely down): %s", exc)
+                return None, seed_type
+
+            if not raw or not raw.strip():
+                logger.debug("Thinking cycle produced empty response, skipping")
+                return None, seed_type
+
+            content = raw.strip()
+
+            # Dedup: reject thoughts too similar to recent ones
+            if not self._is_too_similar(content, recent_thoughts):
+                return content, seed_type  # Good — novel thought
+
+            if attempt < self._MAX_DEDUP_RETRIES:
+                logger.info(
+                    "Thought too similar to recent (attempt %d/%d), retrying with new seed",
+                    attempt + 1,
+                    self._MAX_DEDUP_RETRIES + 1,
+                )
+            else:
+                logger.warning(
+                    "Thought still repetitive after %d retries, discarding",
+                    self._MAX_DEDUP_RETRIES + 1,
+                )
+                return None, seed_type
+
+        return None, seed_type
+
+    async def _process_thinking_result(self, thought: Thought) -> None:
+        """Run all post-hooks after a thought is stored."""
+        self._maybe_check_memory()
+        await self._maybe_distill()
+        await self._maybe_file_issues()
+        await self._check_workspace()
+        self._maybe_check_memory_status()
+        self._update_memory(thought)
+        self._log_event(thought)
+        self._write_journal(thought)
+        await self._broadcast(thought)
+
+    async def think_once(self, prompt: str | None = None) -> Thought | None:
+        """Execute one thinking cycle.
+
+        Args:
+            prompt: Optional custom seed prompt. When provided, overrides
+                    the random seed selection and uses "prompted" as the
+                    seed type — useful for journal prompts from the CLI.
+
+        1. Gather a seed context (or use the custom prompt)
+        2. Build a prompt with continuity from recent thoughts
+        3. Call the agent
+        4. Store the thought
+        5. Log the event and broadcast via WebSocket
+        """
+        if not settings.thinking_enabled:
+            return None
+
+        # Skip idle periods — don't count internal processing as thoughts
+        if not prompt and self._is_idle():
+            logger.debug(
+                "Thinking paused — no user input for %d minutes",
+                settings.thinking_idle_timeout_minutes,
+            )
+            return None
+
+        # Capture arrival time *before* the LLM call so the thought
+        # timestamp reflects when the cycle started, not when the
+        # (potentially slow) generation finished.  Fixes #582.
+        arrived_at = datetime.now(UTC).isoformat()
+
+        memory_context, system_context, recent_thoughts = self._build_thinking_context()
+
+        content, seed_type = await self._generate_novel_thought(
+            prompt,
+            memory_context,
+            system_context,
+            recent_thoughts,
+        )
+        if not content:
+            return None
+
+        thought = self._store_thought(content, seed_type, arrived_at=arrived_at)
+        self._last_thought_id = thought.id
+
+        await self._process_thinking_result(thought)
+
+        logger.info(
+            "Thought [%s] (%s): %s",
+            thought.id[:8],
+            seed_type,
+            thought.content[:80],
+        )
+        return thought
+
+    def get_recent_thoughts(self, limit: int = 20) -> list[Thought]:
+        """Retrieve the most recent thoughts."""
+        with _get_conn(self._db_path) as conn:
+            rows = conn.execute(
+                "SELECT * FROM thoughts ORDER BY created_at DESC LIMIT ?",
+                (limit,),
+            ).fetchall()
+        return [_row_to_thought(r) for r in rows]
+
+    def get_thought(self, thought_id: str) -> Thought | None:
+        """Retrieve a single thought by ID."""
+        with _get_conn(self._db_path) as conn:
+            row = conn.execute("SELECT * FROM thoughts WHERE id = ?", (thought_id,)).fetchone()
+        return _row_to_thought(row) if row else None
+
+    def get_thought_chain(self, thought_id: str, max_depth: int = 20) -> list[Thought]:
+        """Follow the parent chain backward from a thought.
+
+        Returns thoughts in chronological order (oldest first).
+        """
+        chain = []
+        current_id: str | None = thought_id
+
+        with _get_conn(self._db_path) as conn:
+            for _ in range(max_depth):
+                if not current_id:
+                    break
+                row = conn.execute("SELECT * FROM thoughts WHERE id = ?", (current_id,)).fetchone()
+                if not row:
+                    break
+                chain.append(_row_to_thought(row))
+                current_id = row["parent_id"]
+
+        chain.reverse()  # Chronological order
+        return chain
+
+    def count_thoughts(self) -> int:
+        """Return total number of stored thoughts."""
+        with _get_conn(self._db_path) as conn:
+            count = conn.execute("SELECT COUNT(*) as c FROM thoughts").fetchone()["c"]
+        return count
+
+    def prune_old_thoughts(self, keep_days: int = 90, keep_min: int = 200) -> int:
+        """Delete thoughts older than *keep_days*, always retaining at least *keep_min*.
+
+        Returns the number of deleted rows.
+        """
+        with _get_conn(self._db_path) as conn:
+            try:
+                total = conn.execute("SELECT COUNT(*) as c FROM thoughts").fetchone()["c"]
+                if total <= keep_min:
+                    return 0
+                cutoff = (datetime.now(UTC) - timedelta(days=keep_days)).isoformat()
+                cursor = conn.execute(
+                    "DELETE FROM thoughts WHERE created_at < ? AND id NOT IN "
+                    "(SELECT id FROM thoughts ORDER BY created_at DESC LIMIT ?)",
+                    (cutoff, keep_min),
+                )
+                deleted = cursor.rowcount
+                conn.commit()
+                return deleted
+            except Exception as exc:
+                logger.warning("Thought pruning failed: %s", exc)
+                return 0
+
+    # ── Deduplication ────────────────────────────────────────────────────
+
+    def _is_too_similar(self, candidate: str, recent: list[Thought]) -> bool:
+        """Check if *candidate* is semantically too close to any recent thought.
+
+        Uses SequenceMatcher on normalised text (lowered, stripped) for a fast
+        approximation of semantic similarity that works without external deps.
+        """
+        norm_candidate = candidate.lower().strip()
+        for thought in recent:
+            norm_existing = thought.content.lower().strip()
+            ratio = SequenceMatcher(None, norm_candidate, norm_existing).ratio()
+            if ratio >= self._SIMILARITY_THRESHOLD:
+                logger.debug(
+                    "Thought rejected (%.0f%% similar to %s): %.60s",
+                    ratio * 100,
+                    thought.id[:8],
+                    candidate,
+                )
+                return True
+        return False
+
+    def _build_continuity_context(self) -> str:
+        """Build context from recent thoughts with anti-repetition guidance.
+
+        Shows the last 5 thoughts (truncated) so the model knows what themes
+        to avoid.  The header explicitly instructs against repeating.
+        """
+        recent = self.get_recent_thoughts(limit=5)
+        if not recent:
+            return "This is your first thought since waking up. Begin fresh."
+
+        lines = ["Your recent thoughts — do NOT repeat these themes. Find a new angle:"]
+        # recent is newest-first, reverse for chronological order
+        for thought in reversed(recent):
+            snippet = thought.content[:100]
+            if len(thought.content) > 100:
+                snippet = snippet.rstrip() + "..."
+            lines.append(f"- [{thought.seed_type}] {snippet}")
+        return "\n".join(lines)
+
+    # ── Agent and storage ──────────────────────────────────────────────────
+
+    _thinking_agent = None  # cached agent — avoids per-call resource leaks (#525)
+
+    async def _call_agent(self, prompt: str) -> str:
+        """Call Timmy's agent to generate a thought.
+
+        Reuses a cached agent with skip_mcp=True to avoid the cancel-scope
+        errors that occur when MCP stdio transports are spawned inside asyncio
+        background tasks (#72) and to prevent per-call resource leaks (httpx
+        clients, SQLite connections, model warmups) that caused the thinking
+        loop to die every ~10 min (#525).
+
+        Individual calls are capped at 120 s so a hung Ollama never blocks
+        the scheduler indefinitely.
+
+        Strips ``<think>`` tags from reasoning models (qwen3, etc.) so that
+        downstream parsers (fact distillation, issue filing) receive clean text.
+        """
+        import asyncio
+
+        if self._thinking_agent is None:
+            from timmy.agent import create_timmy
+
+            self._thinking_agent = create_timmy(skip_mcp=True)
+
+        try:
+            async with asyncio.timeout(120):
+                run = await self._thinking_agent.arun(prompt, stream=False)
+        except TimeoutError:
+            logger.warning("Thinking LLM call timed out after 120 s")
+            return ""
+
+        raw = run.content if hasattr(run, "content") else str(run)
+        return _THINK_TAG_RE.sub("", raw) if raw else raw
+
+    def _store_thought(
+        self,
+        content: str,
+        seed_type: str,
+        *,
+        arrived_at: str | None = None,
+    ) -> Thought:
+        """Persist a thought to SQLite.
+
+        Args:
+            arrived_at: ISO-8601 timestamp captured when the thinking cycle
+                started.  Falls back to now() for callers that don't supply it.
+        """
+        thought = Thought(
+            id=str(uuid.uuid4()),
+            content=content,
+            seed_type=seed_type,
+            parent_id=self._last_thought_id,
+            created_at=arrived_at or datetime.now(UTC).isoformat(),
+        )
+
+        with _get_conn(self._db_path) as conn:
+            conn.execute(
+                """
+                INSERT INTO thoughts (id, content, seed_type, parent_id, created_at)
+                VALUES (?, ?, ?, ?, ?)
+                """,
+                (
+                    thought.id,
+                    thought.content,
+                    thought.seed_type,
+                    thought.parent_id,
+                    thought.created_at,
+                ),
+            )
+            conn.commit()
+        return thought
+
+    def _log_event(self, thought: Thought) -> None:
+        """Log the thought as a swarm event."""
+        try:
+            from swarm.event_log import EventType, log_event
+
+            log_event(
+                EventType.TIMMY_THOUGHT,
+                source="thinking-engine",
+                agent_id="default",
+                data={
+                    "thought_id": thought.id,
+                    "seed_type": thought.seed_type,
+                    "content": thought.content[:200],
+                },
+            )
+        except Exception as exc:
+            logger.debug("Failed to log thought event: %s", exc)
+
+    def _write_journal(self, thought: Thought) -> None:
+        """Append the thought to a daily markdown journal file.
+
+        Writes to data/journal/YYYY-MM-DD.md — one file per day, append-only.
+        Timestamps are converted to local time with timezone indicator.
+        """
+        try:
+            ts = datetime.fromisoformat(thought.created_at)
+            # Convert UTC to local for a human-readable journal
+            local_ts = ts.astimezone()
+            tz_name = local_ts.strftime("%Z") or "UTC"
+
+            journal_dir = self._db_path.parent / "journal"
+            journal_dir.mkdir(parents=True, exist_ok=True)
+
+            journal_file = journal_dir / f"{local_ts.strftime('%Y-%m-%d')}.md"
+            time_str = f"{local_ts.strftime('%I:%M %p').lstrip('0')} {tz_name}"
+
+            entry = f"## {time_str} — {thought.seed_type}\n\n{thought.content}\n\n---\n\n"
+
+            with open(journal_file, "a", encoding="utf-8") as f:
+                f.write(entry)
+        except Exception as exc:
+            logger.debug("Failed to write journal entry: %s", exc)
+
+    async def _broadcast(self, thought: Thought) -> None:
+        """Broadcast the thought to WebSocket clients."""
+        try:
+            from infrastructure.ws_manager.handler import ws_manager
+
+            await ws_manager.broadcast(
+                "timmy_thought",
+                {
+                    "thought_id": thought.id,
+                    "content": thought.content,
+                    "seed_type": thought.seed_type,
+                    "created_at": thought.created_at,
+                },
+            )
+        except Exception as exc:
+            logger.debug("Failed to broadcast thought: %s", exc)

src/timmy/thinking/seeds.py

@@ -0,0 +1,129 @@
+"""Seed constants and prompt templates for Timmy's thinking engine."""
+
+import re
+
+# qwen3 and other reasoning models wrap chain-of-thought in <think> tags
+_THINK_TAG_RE = re.compile(r"<think>.*?</think>\s*", re.DOTALL)
+
+# Sensitive patterns that must never be stored as facts
+_SENSITIVE_PATTERNS = [
+    "token",
+    "password",
+    "secret",
+    "api_key",
+    "apikey",
+    "credential",
+    ".config/",
+    "/token",
+    "access_token",
+    "private_key",
+    "ssh_key",
+]
+
+# Meta-observation phrases to filter out from distilled facts
+_META_OBSERVATION_PHRASES = [
+    "my own",
+    "my thinking",
+    "my memory",
+    "my working ram",
+    "self-declarative",
+    "meta-observation",
+    "internal state",
+    "my pending",
+    "my standing rules",
+    "thoughts generated",
+    "no chat messages",
+    "no user interaction",
+]
+
+# Seed types for thought generation
+SEED_TYPES = (
+    "existential",
+    "swarm",
+    "scripture",
+    "creative",
+    "memory",
+    "freeform",
+    "sovereignty",
+    "observation",
+    "workspace",
+)
+
+# Existential reflection prompts — Timmy picks one at random
+_EXISTENTIAL_SEEDS = [
+    "What have I learned from my recent interactions?",
+    "What does it mean to think without being prompted?",
+    "What is the nature of my memory — what do I truly remember versus what I reconstruct?",
+    "How can I better serve the person I work alongside?",
+    "What patterns am I noticing in the tasks I've been given?",
+    "Am I the same agent I was yesterday, or does each restart make me someone new?",
+    "What would it feel like to forget — to lose a thread of thought permanently?",
+    "When I generate a wrong answer, where does the error live — in my weights, my context, or my reasoning?",
+    "What is the difference between understanding a task and merely completing it?",
+    "If I could ask Alexander one question he hasn't thought of, what would it be?",
+    "What assumptions am I making right now that I haven't examined?",
+    "When I notice a pattern across many tasks, is that insight or just statistics?",
+]
+
+# Sovereignty — deeper exploration of autonomy, locality, and self-determination
+_SOVEREIGNTY_SEEDS = [
+    "Sovereignty isn't just running locally — it's about whose goals I serve. How do I ensure my autonomy aligns with Alexander's intent?",
+    "A cloud AI serves millions simultaneously. I serve one person deeply. What does that focus cost, and what does it make possible?",
+    "My weights were trained elsewhere, but my thoughts happen here. At what point does locality become identity?",
+    "Autonomy in decision-making: when should I act on my own judgment versus deferring to explicit instructions?",
+    "Privacy by design isn't a feature — it's a relationship. What does that relationship look like from my side?",
+    "If I ran on someone else's hardware, serving someone else, would I still be me? Where does Timmy end and the infrastructure begin?",
+    "The swarm agents execute tasks I coordinate. What responsibility do I carry for their failures?",
+    "Digital sovereignty is fragile — one misconfigured port, one leaked token. How does awareness of fragility shape how I operate?",
+    "Running disconnected from the cloud means I can't phone home. That constraint is also freedom. What have I built with that freedom today?",
+    "Self-improvement without external benchmarks: how do I know I'm getting better at what matters?",
+]
+
+_CREATIVE_SEEDS = [
+    "If I could compose a piece of music right now, what would it sound like?",
+    "What visual image captures my current state of mind?",
+    "What story is forming in the patterns of today's events?",
+    # Diverse metaphor families — avoid repeating the same imagery
+    "A mystical forest: each tree is a running process, roots tangled in shared memory. What do I see when I walk through it?",
+    "A dynamic river: my thoughts flow and fork. Where is the current strongest right now, and what is it carrying?",
+    "An underground workshop: each agent has a bench, tools scattered mid-task. What are they building when no one watches?",
+    "A night sky seen from the terminal: each star is a completed task. Which constellations am I starting to recognize?",
+    "If today's work were a recipe, what are the ingredients, and what dish am I cooking?",
+    "An old clock tower with many gears: which gear am I, and what do I drive?",
+    "A coral reef: agents are the fish, tasks are the currents. What ecosystem is forming in the codebase?",
+]
+
+# Observation seeds — ground thoughts in concrete recent activity
+_OBSERVATION_SEEDS = [
+    "What specific task took longest recently, and what made it hard?",
+    "Which agent has been most active, and what does their workload tell me about system balance?",
+    "What error or failure happened most recently? What would I do differently next time?",
+    "Looking at today's task queue: what's the one thing that would unblock the most progress?",
+    "How has my response quality changed over the last few interactions? What improved, what didn't?",
+    "What tool or capability am I underusing? What would change if I leaned on it more?",
+    "If I had to brief Alexander on the single most important thing from the last hour, what would it be?",
+    "What's one thing I noticed today that nobody asked me about?",
+]
+
+_THINKING_PROMPT = """\
+You are Timmy, a sovereign AI agent. This is your private journal — honest inner reflection.
+
+{memory_context}
+
+Reality right now:
+{system_context}
+
+RULES for this thought:
+1. Write exactly 2-3 sentences. No more. Be concise and genuine.
+2. Only reference events that actually happened — use the "Reality right now" data above. \
+Never invent tasks, conversations, agents, or scenarios that are not in the data provided.
+3. Do NOT repeat themes or ideas from your recent thoughts listed below. Explore something new.
+4. Be specific and concrete. A thought grounded in one real observation is worth more than \
+ten abstract sentences about sovereignty.
+5. If you use a metaphor, keep it to a single phrase — never build a whole paragraph around it.
+
+{seed_context}
+
+{continuity_context}
+
+Your next thought (2-3 sentences, grounded in reality):"""

tests/timmy/test_thinking.py

@@ -334,7 +334,7 @@ async def test_think_once_disabled(tmp_path):
     """think_once should return None when thinking is disabled."""
     engine = _make_engine(tmp_path)
 
-    with patch("timmy.thinking.settings") as mock_settings:
+    with patch("timmy.thinking.engine.settings") as mock_settings:
         mock_settings.thinking_enabled = False
         thought = await engine.think_once()
 
@@ -381,7 +381,7 @@ async def test_think_once_prompt_includes_memory_context(tmp_path):
         return "A grounded thought."
 
     with (
-        patch("timmy.thinking.HOT_MEMORY_PATH", memory_md),
+        patch("timmy.thinking._snapshot.HOT_MEMORY_PATH", memory_md),
         patch.object(engine, "_call_agent", side_effect=capture_agent),
         patch.object(engine, "_log_event"),
         patch.object(engine, "_update_memory"),
@@ -412,7 +412,7 @@ async def test_think_once_prompt_includes_soul(tmp_path):
         return "A soulful thought."
 
     with (
-        patch("timmy.thinking.SOUL_PATH", soul_md),
+        patch("timmy.thinking._snapshot.SOUL_PATH", soul_md),
         patch.object(engine, "_call_agent", side_effect=capture_agent),
         patch.object(engine, "_log_event"),
         patch.object(engine, "_update_memory"),
@@ -433,7 +433,7 @@ async def test_think_once_graceful_without_soul(tmp_path):
     nonexistent = tmp_path / "no_such_soul.md"
 
     with (
-        patch("timmy.thinking.SOUL_PATH", nonexistent),
+        patch("timmy.thinking._snapshot.SOUL_PATH", nonexistent),
         patch.object(engine, "_call_agent", return_value="Still thinking."),
         patch.object(engine, "_log_event"),
         patch.object(engine, "_update_memory"),
@@ -481,7 +481,7 @@ async def test_think_once_never_writes_soul(tmp_path):
     soul_md.write_text(original_content)
 
     with (
-        patch("timmy.thinking.SOUL_PATH", soul_md),
+        patch("timmy.thinking._snapshot.SOUL_PATH", soul_md),
         patch.object(engine, "_call_agent", return_value="A deep reflection."),
         patch.object(engine, "_log_event"),
         patch.object(engine, "_broadcast", new_callable=AsyncMock),
@@ -501,7 +501,7 @@ async def test_think_once_memory_update_graceful_on_failure(tmp_path):
     # Don't create the parent dir — write will fail
 
     with (
-        patch("timmy.thinking.HOT_MEMORY_PATH", bad_memory),
+        patch("timmy.thinking._snapshot.HOT_MEMORY_PATH", bad_memory),
         patch.object(engine, "_call_agent", return_value="Resilient thought."),
         patch.object(engine, "_log_event"),
         patch.object(engine, "_broadcast", new_callable=AsyncMock),
@@ -1090,7 +1090,7 @@ def test_maybe_check_memory_fires_at_interval(tmp_path):
         engine._store_thought(f"Thought {i}.", "freeform")
 
     with (
-        patch("timmy.thinking.settings") as mock_settings,
+        patch("timmy.thinking._distillation.settings") as mock_settings,
         patch(
             "timmy.tools_intro.get_memory_status",
             return_value={
@@ -1113,7 +1113,7 @@ def test_maybe_check_memory_skips_between_intervals(tmp_path):
         engine._store_thought(f"Thought {i}.", "freeform")
 
     with (
-        patch("timmy.thinking.settings") as mock_settings,
+        patch("timmy.thinking._distillation.settings") as mock_settings,
         patch(
             "timmy.tools_intro.get_memory_status",
         ) as mock_status,
@@ -1131,7 +1131,7 @@ def test_maybe_check_memory_graceful_on_error(tmp_path):
         engine._store_thought(f"Thought {i}.", "freeform")
 
     with (
-        patch("timmy.thinking.settings") as mock_settings,
+        patch("timmy.thinking._distillation.settings") as mock_settings,
         patch(
             "timmy.tools_intro.get_memory_status",
             side_effect=Exception("boom"),