Claude Code Memory Compiler

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Cole Medin 2026-04-06 09:26:30 -05:00
commit f83d38d787
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.claude/settings.json Normal file
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{
"hooks": {
"SessionStart": [
{
"matcher": "",
"hooks": [
{
"type": "command",
"command": "uv run python hooks/session-start.py",
"timeout": 15
}
]
}
],
"PreCompact": [
{
"matcher": "",
"hooks": [
{
"type": "command",
"command": "uv run python hooks/pre-compact.py",
"timeout": 10
}
]
}
],
"SessionEnd": [
{
"matcher": "",
"hooks": [
{
"type": "command",
"command": "uv run python hooks/session-end.py",
"timeout": 10
}
]
}
]
}
}

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# Python
__pycache__/
*.pyc
.venv/
# Runtime state (regenerated by scripts)
scripts/state.json
scripts/last-flush.json
scripts/flush.log
scripts/compile.log
scripts/session-flush-*
scripts/flush-context-*
# Generated content (built up per-user by hooks and scripts)
daily/
knowledge/
# Reports (regenerated by lint)
reports/
# uv lock (regenerated by uv sync)
scripts/uv.lock
# Claude Code local settings
.claude/settings.local.json
# OS files
.DS_Store
Thumbs.db

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# AGENTS.md - Personal Knowledge Base Schema
> Adapted from [Andrej Karpathy's LLM Knowledge Base](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f) architecture.
> Instead of ingesting external articles, this system compiles knowledge from your own AI conversations.
## The Compiler Analogy
```
daily/ = source code (your conversations - the raw material)
LLM = compiler (extracts and organizes knowledge)
knowledge/ = executable (structured, queryable knowledge base)
lint = test suite (health checks for consistency)
queries = runtime (using the knowledge)
```
You don't manually organize your knowledge. You have conversations, and the LLM handles the synthesis, cross-referencing, and maintenance.
---
## Architecture
### Layer 1: `daily/` - Conversation Logs (Immutable Source)
Daily logs capture what happened in your AI coding sessions. These are the "raw sources" - append-only, never edited after the fact.
```
daily/
├── 2026-04-01.md
├── 2026-04-02.md
├── ...
```
Each file follows this format:
```markdown
# Daily Log: YYYY-MM-DD
## Sessions
### Session (HH:MM) - Brief Title
**Context:** What the user was working on.
**Key Exchanges:**
- User asked about X, assistant explained Y
- Decided to use Z approach because...
- Discovered that W doesn't work when...
**Decisions Made:**
- Chose library X over Y because...
- Architecture: went with pattern Z
**Lessons Learned:**
- Always do X before Y to avoid...
- The gotcha with Z is that...
**Action Items:**
- [ ] Follow up on X
- [ ] Refactor Y when time permits
```
### Layer 2: `knowledge/` - Compiled Knowledge (LLM-Owned)
The LLM owns this directory entirely. Humans read it but rarely edit it directly.
```
knowledge/
├── index.md # Master catalog - every article with one-line summary
├── log.md # Append-only chronological build log
├── concepts/ # Atomic knowledge articles
├── connections/ # Cross-cutting insights linking 2+ concepts
└── qa/ # Filed query answers (compounding knowledge)
```
### Layer 3: This File (AGENTS.md)
The schema that tells the LLM how to compile and maintain the knowledge base. This is the "compiler specification."
---
## Structural Files
### `knowledge/index.md` - Master Catalog
A table listing every knowledge article. This is the primary retrieval mechanism - the LLM reads this FIRST when answering any query, then selects relevant articles to read in full.
Format:
```markdown
# Knowledge Base Index
| Article | Summary | Compiled From | Updated |
|---------|---------|---------------|---------|
| [[concepts/supabase-auth]] | Row-level security patterns and JWT gotchas | daily/2026-04-02.md | 2026-04-02 |
| [[connections/auth-and-webhooks]] | Token verification patterns shared across Supabase auth and Stripe webhooks | daily/2026-04-02.md, daily/2026-04-04.md | 2026-04-04 |
```
### `knowledge/log.md` - Build Log
Append-only chronological record of every compile, query, and lint operation.
Format:
```markdown
# Build Log
## [2026-04-01T14:30:00] compile | Daily Log 2026-04-01
- Source: daily/2026-04-01.md
- Articles created: [[concepts/nextjs-project-structure]], [[concepts/tailwind-setup]]
- Articles updated: (none)
## [2026-04-02T09:00:00] query | "How do I handle auth redirects?"
- Consulted: [[concepts/supabase-auth]], [[concepts/nextjs-middleware]]
- Filed to: [[qa/auth-redirect-handling]]
```
---
## Article Formats
### Concept Articles (`knowledge/concepts/`)
One article per atomic piece of knowledge. These are facts, patterns, decisions, preferences, and lessons extracted from your conversations.
```markdown
---
title: "Concept Name"
aliases: [alternate-name, abbreviation]
tags: [domain, topic]
sources:
- "daily/2026-04-01.md"
- "daily/2026-04-03.md"
created: 2026-04-01
updated: 2026-04-03
---
# Concept Name
[2-4 sentence core explanation]
## Key Points
- [Bullet points, each self-contained]
## Details
[Deeper explanation, encyclopedia-style paragraphs]
## Related Concepts
- [[concepts/related-concept]] - How it connects
## Sources
- [[daily/2026-04-01.md]] - Initial discovery during project setup
- [[daily/2026-04-03.md]] - Updated after debugging session
```
### Connection Articles (`knowledge/connections/`)
Cross-cutting synthesis linking 2+ concepts. Created when a conversation reveals a non-obvious relationship.
```markdown
---
title: "Connection: X and Y"
connects:
- "concepts/concept-x"
- "concepts/concept-y"
sources:
- "daily/2026-04-04.md"
created: 2026-04-04
updated: 2026-04-04
---
# Connection: X and Y
## The Connection
[What links these concepts]
## Key Insight
[The non-obvious relationship discovered]
## Evidence
[Specific examples from conversations]
## Related Concepts
- [[concepts/concept-x]]
- [[concepts/concept-y]]
```
### Q&A Articles (`knowledge/qa/`)
Filed answers from queries. Every complex question answered by the system can be permanently stored, making future queries smarter.
```markdown
---
title: "Q: Original Question"
question: "The exact question asked"
consulted:
- "concepts/article-1"
- "concepts/article-2"
filed: 2026-04-05
---
# Q: Original Question
## Answer
[The synthesized answer with [[wikilinks]] to sources]
## Sources Consulted
- [[concepts/article-1]] - Relevant because...
- [[concepts/article-2]] - Provided context on...
## Follow-Up Questions
- What about edge case X?
- How does this change if Y?
```
---
## Core Operations
### 1. Compile (daily/ -> knowledge/)
When processing a daily log:
1. Read the daily log file
2. Read `knowledge/index.md` to understand current knowledge state
3. Read existing articles that may need updating
4. For each piece of knowledge found in the log:
- If an existing concept article covers this topic: UPDATE it with new information, add the daily log as a source
- If it's a new topic: CREATE a new `concepts/` article
5. If the log reveals a non-obvious connection between 2+ existing concepts: CREATE a `connections/` article
6. UPDATE `knowledge/index.md` with new/modified entries
7. APPEND to `knowledge/log.md`
**Important guidelines:**
- A single daily log may touch 3-10 knowledge articles
- Prefer updating existing articles over creating near-duplicates
- Use Obsidian-style `[[wikilinks]]` with full relative paths from knowledge/
- Write in encyclopedia style - factual, concise, self-contained
- Every article must have YAML frontmatter
- Every article must link back to its source daily logs
### 2. Query (Ask the Knowledge Base)
1. Read `knowledge/index.md` (the master catalog)
2. Based on the question, identify 3-10 relevant articles from the index
3. Read those articles in full
4. Synthesize an answer with `[[wikilink]]` citations
5. If `--file-back` is specified: create a `knowledge/qa/` article and update index.md and log.md
**Why this works without RAG:** At personal knowledge base scale (50-500 articles), the LLM reading a structured index outperforms cosine similarity. The LLM understands what the question is really asking and selects pages accordingly. Embeddings find similar words; the LLM finds relevant concepts.
### 3. Lint (Health Checks)
Seven checks, run periodically:
1. **Broken links** - `[[wikilinks]]` pointing to non-existent articles
2. **Orphan pages** - Articles with zero inbound links from other articles
3. **Orphan sources** - Daily logs that haven't been compiled yet
4. **Stale articles** - Source daily log changed since article was last compiled
5. **Contradictions** - Conflicting claims across articles (requires LLM judgment)
6. **Missing backlinks** - A links to B but B doesn't link back to A
7. **Sparse articles** - Below 200 words, likely incomplete
Output: a markdown report with severity levels (error, warning, suggestion).
---
## Conventions
- **Wikilinks:** Use Obsidian-style `[[path/to/article]]` without `.md` extension
- **Writing style:** Encyclopedia-style, factual, third-person where appropriate
- **Dates:** ISO 8601 (YYYY-MM-DD for dates, full ISO for timestamps in log.md)
- **File naming:** lowercase, hyphens for spaces (e.g., `supabase-row-level-security.md`)
- **Frontmatter:** Every article must have YAML frontmatter with at minimum: title, sources, created, updated
- **Sources:** Always link back to the daily log(s) that contributed to an article
---
## Full Project Structure
```
llm-personal-kb/
|-- .claude/
| |-- settings.json # Hook configuration (auto-activates in Claude Code)
|-- .gitignore # Excludes runtime state, temp files, caches
|-- AGENTS.md # This file - schema + full technical reference
|-- README.md # Concise overview + quick start
|-- pyproject.toml # Dependencies (at root so hooks can find it)
|-- daily/ # "Source code" - conversation logs (immutable)
|-- knowledge/ # "Executable" - compiled knowledge (LLM-owned)
| |-- index.md # Master catalog - THE retrieval mechanism
| |-- log.md # Append-only build log
| |-- concepts/ # Atomic knowledge articles
| |-- connections/ # Cross-cutting insights linking 2+ concepts
| |-- qa/ # Filed query answers (compounding knowledge)
|-- scripts/ # CLI tools
| |-- compile.py # Compile daily logs -> knowledge articles
| |-- query.py # Ask questions (index-guided, no RAG)
| |-- lint.py # 7 health checks
| |-- flush.py # Extract memories from conversations (background)
| |-- config.py # Path constants
| |-- utils.py # Shared helpers
|-- hooks/ # Claude Code hooks
| |-- session-start.py # Injects knowledge into every session
| |-- session-end.py # Extracts conversation -> daily log
| |-- pre-compact.py # Safety net: captures context before compaction
|-- reports/ # Lint reports (gitignored)
```
---
## Hook System (Automatic Capture)
Hooks are configured in `.claude/settings.json` and fire automatically when you use Claude Code in this project.
### `.claude/settings.json` Format
```json
{
"hooks": {
"SessionStart": [{ "matcher": "", "hooks": [{ "type": "command", "command": "uv run python hooks/session-start.py", "timeout": 15 }] }],
"PreCompact": [{ "matcher": "", "hooks": [{ "type": "command", "command": "uv run python hooks/pre-compact.py", "timeout": 10 }] }],
"SessionEnd": [{ "matcher": "", "hooks": [{ "type": "command", "command": "uv run python hooks/session-end.py", "timeout": 10 }] }]
}
}
```
Commands use simple relative paths from the project root. Empty `matcher` catches all events.
### Hook Details
**`session-start.py`** (SessionStart)
- Pure local I/O, no API calls, runs in under 1 second
- Reads `knowledge/index.md` and the most recent daily log
- Outputs JSON to stdout: `{"hookSpecificOutput": {"hookEventName": "SessionStart", "additionalContext": "..."}}`
- Claude sees the knowledge base index at the start of every session
- Max context: 20,000 characters
**`session-end.py`** (SessionEnd)
- Reads hook input from stdin (JSON with `session_id`, `transcript_path`, `cwd`)
- Copies the raw JSONL transcript to a temp file (no parsing in the hook - keeps it fast)
- Spawns `flush.py` as a fully detached background process
- Recursion guard: exits immediately if `CLAUDE_INVOKED_BY` env var is set
**`pre-compact.py`** (PreCompact)
- Same architecture as session-end.py
- Fires before Claude Code auto-compacts the context window
- Guards against empty `transcript_path` (known Claude Code bug #13668)
- Critical for long sessions: captures context before summarization discards it
**Why both PreCompact and SessionEnd?** Long-running sessions may trigger multiple auto-compactions before you close the session. Without PreCompact, intermediate context is lost to summarization before SessionEnd ever fires.
### Background Flush Process (`flush.py`)
Spawned by both hooks as a fully detached background process:
- **Windows:** `CREATE_NEW_PROCESS_GROUP | DETACHED_PROCESS` flags
- **Mac/Linux:** `start_new_session=True`
This ensures flush.py survives after Claude Code's hook process exits.
**What flush.py does:**
1. Sets `CLAUDE_INVOKED_BY=memory_flush` env var (prevents recursive hook firing)
2. Reads the pre-extracted conversation context from the temp `.md` file
3. Skips if context is empty or if same session was flushed within 60 seconds (deduplication)
4. Calls Claude Agent SDK (`query()` with `allowed_tools=[]`, `max_turns=2`)
5. Claude decides what's worth saving - returns structured bullet points or `FLUSH_OK`
6. Appends result to `daily/YYYY-MM-DD.md`
7. Cleans up temp context file
8. **End-of-day auto-compilation:** If it's past 6 PM local time (`COMPILE_AFTER_HOUR = 18`) and today's daily log has changed since its last compilation (hash comparison against `state.json`), spawns `compile.py` as another detached background process. This means compilation happens automatically once a day without needing a cron job or manual trigger.
### JSONL Transcript Format
Claude Code stores conversations as `.jsonl` files. Messages are nested under a `message` key:
```python
entry = json.loads(line)
msg = entry.get("message", {})
role = msg.get("role", "") # "user" or "assistant"
content = msg.get("content", "") # string or list of content blocks
```
Content can be a string or a list of blocks (`{"type": "text", "text": "..."}` dicts).
---
## Script Details
### compile.py - The Compiler
Uses the Claude Agent SDK's async streaming `query()`:
```python
async for message in query(
prompt=compile_prompt,
options=ClaudeAgentOptions(
cwd=str(ROOT_DIR),
system_prompt={"type": "preset", "preset": "claude_code"},
allowed_tools=["Read", "Write", "Edit", "Glob", "Grep"],
permission_mode="acceptEdits",
max_turns=30,
),
):
```
- Builds a prompt with: AGENTS.md schema, current index, all existing articles, and the daily log
- Claude reads the daily log, decides what concepts to extract, and writes files directly
- `permission_mode="acceptEdits"` auto-approves all file operations
- Incremental: tracks SHA-256 hashes of daily logs in `state.json`, skips unchanged files
- Cost: ~$0.45-0.65 per daily log (increases as KB grows)
**CLI:**
```bash
uv run python scripts/compile.py # compile new/changed only
uv run python scripts/compile.py --all # force recompile everything
uv run python scripts/compile.py --file daily/2026-04-01.md
uv run python scripts/compile.py --dry-run
```
### query.py - Index-Guided Retrieval
Loads the entire knowledge base into context (index + all articles). No RAG.
At personal KB scale (50-500 articles), the LLM reading a structured index outperforms vector similarity. The LLM understands what you're really asking; cosine similarity just finds similar words.
**CLI:**
```bash
uv run python scripts/query.py "What auth patterns do I use?"
uv run python scripts/query.py "What's my error handling strategy?" --file-back
```
With `--file-back`, creates a Q&A article in `knowledge/qa/` and updates the index and log. This is the compounding loop - every question makes the KB smarter.
### lint.py - Health Checks
Seven checks:
| Check | Type | Catches |
|-------|------|---------|
| Broken links | Structural | `[[wikilinks]]` to non-existent articles |
| Orphan pages | Structural | Articles with zero inbound links |
| Orphan sources | Structural | Daily logs not yet compiled |
| Stale articles | Structural | Source logs changed since compilation |
| Missing backlinks | Structural | A links to B but B doesn't link back |
| Sparse articles | Structural | Under 200 words |
| Contradictions | LLM | Conflicting claims across articles |
**CLI:**
```bash
uv run python scripts/lint.py # all checks
uv run python scripts/lint.py --structural-only # skip LLM check (free)
```
Reports saved to `reports/lint-YYYY-MM-DD.md`.
---
## State Tracking
`scripts/state.json` tracks:
- `ingested` - map of daily log filenames to SHA-256 hashes, compilation timestamps, and costs
- `query_count` - total queries run
- `last_lint` - timestamp of most recent lint
- `total_cost` - cumulative API cost
`scripts/last-flush.json` tracks flush deduplication (session_id + timestamp).
Both are gitignored and regenerated automatically.
---
## Dependencies
`pyproject.toml` (at project root):
- `claude-agent-sdk>=0.1.29` - Claude Agent SDK for LLM calls with tool use
- `python-dotenv>=1.0.0` - Environment variable management
- `tzdata>=2024.1` - Timezone data
- Python 3.12+, managed by [uv](https://docs.astral.sh/uv/)
No API key needed - uses Claude Code's built-in credentials at `~/.claude/.credentials.json`.
---
## Costs
| Operation | Cost |
|-----------|------|
| Compile one daily log | $0.45-0.65 |
| Query (no file-back) | ~$0.15-0.25 |
| Query (with file-back) | ~$0.25-0.40 |
| Full lint (with contradictions) | ~$0.15-0.25 |
| Structural lint only | $0.00 |
| Memory flush (per session) | ~$0.02-0.05 |
---
## Customization
### Additional Article Types
Add directories like `people/`, `projects/`, `tools/` to `knowledge/`. Define the article format in this file (AGENTS.md) and update `utils.py`'s `list_wiki_articles()` to include them.
### Obsidian Integration
The knowledge base is pure markdown with `[[wikilinks]]` - works natively in Obsidian. Point a vault at `knowledge/` for graph view, backlinks, and search.
### Scaling Beyond Index-Guided Retrieval
At ~2,000+ articles / ~2M+ tokens, the index becomes too large for the context window. At that point, add hybrid RAG (keyword + semantic search) as a retrieval layer before the LLM. See Karpathy's recommendation of `qmd` by Tobi Lutke for search at scale.

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# LLM Personal Knowledge Base
**Your AI conversations compile themselves into a searchable knowledge base.**
Adapted from [Karpathy's LLM Knowledge Base](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f) architecture, but instead of clipping web articles, the raw data is your own conversations with Claude Code. When a session ends (or auto-compacts mid-session), Claude Code hooks capture the conversation transcript and spawn a background process that uses the [Claude Agent SDK](https://github.com/anthropics/claude-agent-sdk) to extract the important stuff - decisions, lessons learned, patterns, gotchas - and appends it to a daily log. You then compile those daily logs into structured, cross-referenced knowledge articles organized by concept. Retrieval uses a simple index file instead of RAG - no vector database, no embeddings, just markdown.
Anthropic has clarified that personal use of the Claude Agent SDK is covered under your existing Claude subscription (Max, Team, or Enterprise) - no separate API credits needed. Unlike OpenClaw, which requires API billing for its memory flush, this runs on your subscription.
## Quick Start
Tell your AI coding agent:
> "Clone https://github.com/coleam00/llm-personal-kb into this project. Set up the Claude Code hooks so my conversations automatically get captured into daily logs, compiled into a knowledge base, and injected back into future sessions. Read the AGENTS.md for the full technical reference on how everything works."
The agent will:
1. Clone the repo and run `uv sync` to install dependencies
2. Copy `.claude/settings.json` into your project (or merge the hooks into your existing settings)
3. The hooks activate automatically next time you open Claude Code
From there, your conversations start accumulating. After 6 PM local time, the next session flush automatically triggers compilation of that day's logs into knowledge articles. You can also run `uv run python scripts/compile.py` manually at any time.
## How It Works
```
Conversation -> SessionEnd/PreCompact hooks -> flush.py extracts knowledge
-> daily/YYYY-MM-DD.md -> compile.py -> knowledge/concepts/, connections/, qa/
-> SessionStart hook injects index into next session -> cycle repeats
```
- **Hooks** capture conversations automatically (session end + pre-compaction safety net)
- **flush.py** calls the Claude Agent SDK to decide what's worth saving, and after 6 PM triggers end-of-day compilation automatically
- **compile.py** turns daily logs into organized concept articles with cross-references (triggered automatically or run manually)
- **query.py** answers questions using index-guided retrieval (no RAG needed at personal scale)
- **lint.py** runs 7 health checks (broken links, orphans, contradictions, staleness)
## Key Commands
```bash
uv run python scripts/compile.py # compile new daily logs
uv run python scripts/query.py "question" # ask the knowledge base
uv run python scripts/query.py "question" --file-back # ask + save answer back
uv run python scripts/lint.py # run health checks
uv run python scripts/lint.py --structural-only # free structural checks only
```
## Why No RAG?
Karpathy's insight: at personal scale (50-500 articles), the LLM reading a structured `index.md` outperforms vector similarity. The LLM understands what you're really asking; cosine similarity just finds similar words. RAG becomes necessary at ~2,000+ articles when the index exceeds the context window.
## Technical Reference
See **[AGENTS.md](AGENTS.md)** for the complete technical reference: article formats, hook architecture, script internals, cross-platform details, costs, and customization options. AGENTS.md is designed to give an AI agent everything it needs to understand, modify, or rebuild the system.

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"""
PreCompact hook - captures conversation transcript before auto-compaction.
When Claude Code's context window fills up, it auto-compacts (summarizes and
discards detail). This hook fires BEFORE that happens, extracting conversation
context and spawning flush.py to extract knowledge that would otherwise
be lost to summarization.
The hook itself does NO API calls - only local file I/O for speed (<10s).
"""
from __future__ import annotations
import json
import logging
import os
import re
import subprocess
import sys
from datetime import datetime, timezone
from pathlib import Path
# Recursion guard
if os.environ.get("CLAUDE_INVOKED_BY"):
sys.exit(0)
ROOT = Path(__file__).resolve().parent.parent
SCRIPTS_DIR = ROOT / "scripts"
STATE_DIR = SCRIPTS_DIR
logging.basicConfig(
filename=str(SCRIPTS_DIR / "flush.log"),
level=logging.INFO,
format="%(asctime)s %(levelname)s [pre-compact] %(message)s",
datefmt="%Y-%m-%d %H:%M:%S",
)
MAX_TURNS = 30
MAX_CONTEXT_CHARS = 15_000
MIN_TURNS_TO_FLUSH = 5
def extract_conversation_context(transcript_path: Path) -> tuple[str, int]:
"""Read JSONL transcript and extract last ~N conversation turns as markdown."""
turns: list[str] = []
with open(transcript_path, encoding="utf-8") as f:
for line in f:
line = line.strip()
if not line:
continue
try:
entry = json.loads(line)
except json.JSONDecodeError:
continue
msg = entry.get("message", {})
if isinstance(msg, dict):
role = msg.get("role", "")
content = msg.get("content", "")
else:
role = entry.get("role", "")
content = entry.get("content", "")
if role not in ("user", "assistant"):
continue
if isinstance(content, list):
text_parts = []
for block in content:
if isinstance(block, dict) and block.get("type") == "text":
text_parts.append(block.get("text", ""))
elif isinstance(block, str):
text_parts.append(block)
content = "\n".join(text_parts)
if isinstance(content, str) and content.strip():
label = "User" if role == "user" else "Assistant"
turns.append(f"**{label}:** {content.strip()}\n")
recent = turns[-MAX_TURNS:]
context = "\n".join(recent)
if len(context) > MAX_CONTEXT_CHARS:
context = context[-MAX_CONTEXT_CHARS:]
boundary = context.find("\n**")
if boundary > 0:
context = context[boundary + 1 :]
return context, len(recent)
def main() -> None:
# Read hook input from stdin
try:
raw_input = sys.stdin.read()
try:
hook_input: dict = json.loads(raw_input)
except json.JSONDecodeError:
fixed_input = re.sub(r'(?<!\\)\\(?!["\\])', r'\\\\', raw_input)
hook_input = json.loads(fixed_input)
except (json.JSONDecodeError, ValueError, EOFError) as e:
logging.error("Failed to parse stdin: %s", e)
return
session_id = hook_input.get("session_id", "unknown")
transcript_path_str = hook_input.get("transcript_path", "")
logging.info("PreCompact fired: session=%s", session_id)
# transcript_path can be empty (known Claude Code bug #13668)
if not transcript_path_str or not isinstance(transcript_path_str, str):
logging.info("SKIP: no transcript path")
return
transcript_path = Path(transcript_path_str)
if not transcript_path.exists():
logging.info("SKIP: transcript missing: %s", transcript_path_str)
return
# Extract conversation context in the hook
try:
context, turn_count = extract_conversation_context(transcript_path)
except Exception as e:
logging.error("Context extraction failed: %s", e)
return
if not context.strip():
logging.info("SKIP: empty context")
return
if turn_count < MIN_TURNS_TO_FLUSH:
logging.info("SKIP: only %d turns (min %d)", turn_count, MIN_TURNS_TO_FLUSH)
return
# Write context to a temp file for the background process
timestamp = datetime.now(timezone.utc).astimezone().strftime("%Y%m%d-%H%M%S")
context_file = STATE_DIR / f"flush-context-{session_id}-{timestamp}.md"
context_file.write_text(context, encoding="utf-8")
# Spawn flush.py as a background process
flush_script = SCRIPTS_DIR / "flush.py"
cmd = [
"uv",
"run",
"--directory",
str(ROOT),
"python",
str(flush_script),
str(context_file),
session_id,
]
creation_flags = subprocess.CREATE_NO_WINDOW if sys.platform == "win32" else 0
try:
subprocess.Popen(
cmd,
stdout=subprocess.DEVNULL,
stderr=subprocess.DEVNULL,
creationflags=creation_flags,
)
logging.info("Spawned flush.py for session %s (%d turns, %d chars)", session_id, turn_count, len(context))
except Exception as e:
logging.error("Failed to spawn flush.py: %s", e)
if __name__ == "__main__":
main()

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"""
SessionEnd hook - captures conversation transcript for memory extraction.
When a Claude Code session ends, this hook reads the transcript path from
stdin, extracts conversation context, and spawns flush.py as a background
process to extract knowledge into the daily log.
The hook itself does NO API calls - only local file I/O for speed (<10s).
"""
from __future__ import annotations
import json
import logging
import os
import re
import subprocess
import sys
from datetime import datetime, timezone
from pathlib import Path
# Recursion guard: if we were spawned by flush.py (which calls Agent SDK,
# which runs Claude Code, which would fire this hook again), exit immediately.
if os.environ.get("CLAUDE_INVOKED_BY"):
sys.exit(0)
ROOT = Path(__file__).resolve().parent.parent
DAILY_DIR = ROOT / "daily"
SCRIPTS_DIR = ROOT / "scripts"
STATE_DIR = SCRIPTS_DIR
logging.basicConfig(
filename=str(SCRIPTS_DIR / "flush.log"),
level=logging.INFO,
format="%(asctime)s %(levelname)s [hook] %(message)s",
datefmt="%Y-%m-%d %H:%M:%S",
)
MAX_TURNS = 30
MAX_CONTEXT_CHARS = 15_000
MIN_TURNS_TO_FLUSH = 1
def extract_conversation_context(transcript_path: Path) -> tuple[str, int]:
"""Read JSONL transcript and extract last ~N conversation turns as markdown."""
turns: list[str] = []
with open(transcript_path, encoding="utf-8") as f:
for line in f:
line = line.strip()
if not line:
continue
try:
entry = json.loads(line)
except json.JSONDecodeError:
continue
msg = entry.get("message", {})
if isinstance(msg, dict):
role = msg.get("role", "")
content = msg.get("content", "")
else:
role = entry.get("role", "")
content = entry.get("content", "")
if role not in ("user", "assistant"):
continue
if isinstance(content, list):
text_parts = []
for block in content:
if isinstance(block, dict) and block.get("type") == "text":
text_parts.append(block.get("text", ""))
elif isinstance(block, str):
text_parts.append(block)
content = "\n".join(text_parts)
if isinstance(content, str) and content.strip():
label = "User" if role == "user" else "Assistant"
turns.append(f"**{label}:** {content.strip()}\n")
recent = turns[-MAX_TURNS:]
context = "\n".join(recent)
if len(context) > MAX_CONTEXT_CHARS:
context = context[-MAX_CONTEXT_CHARS:]
boundary = context.find("\n**")
if boundary > 0:
context = context[boundary + 1 :]
return context, len(recent)
def main() -> None:
# Read hook input from stdin
# Claude Code on Windows may pass paths with unescaped backslashes
try:
raw_input = sys.stdin.read()
try:
hook_input: dict = json.loads(raw_input)
except json.JSONDecodeError:
fixed_input = re.sub(r'(?<!\\)\\(?!["\\])', r'\\\\', raw_input)
hook_input = json.loads(fixed_input)
except (json.JSONDecodeError, ValueError, EOFError) as e:
logging.error("Failed to parse stdin: %s", e)
return
session_id = hook_input.get("session_id", "unknown")
source = hook_input.get("source", "unknown")
transcript_path_str = hook_input.get("transcript_path", "")
logging.info("SessionEnd fired: session=%s source=%s", session_id, source)
if not transcript_path_str or not isinstance(transcript_path_str, str):
logging.info("SKIP: no transcript path")
return
transcript_path = Path(transcript_path_str)
if not transcript_path.exists():
logging.info("SKIP: transcript missing: %s", transcript_path_str)
return
# Extract conversation context in the hook (fast, no API calls)
try:
context, turn_count = extract_conversation_context(transcript_path)
except Exception as e:
logging.error("Context extraction failed: %s", e)
return
if not context.strip():
logging.info("SKIP: empty context")
return
if turn_count < MIN_TURNS_TO_FLUSH:
logging.info("SKIP: only %d turns (min %d)", turn_count, MIN_TURNS_TO_FLUSH)
return
# Write context to a temp file for the background process
timestamp = datetime.now(timezone.utc).astimezone().strftime("%Y%m%d-%H%M%S")
context_file = STATE_DIR / f"session-flush-{session_id}-{timestamp}.md"
context_file.write_text(context, encoding="utf-8")
# Spawn flush.py as a background process
flush_script = SCRIPTS_DIR / "flush.py"
cmd = [
"uv",
"run",
"--directory",
str(ROOT),
"python",
str(flush_script),
str(context_file),
session_id,
]
# On Windows, use CREATE_NO_WINDOW to avoid flash console window.
# Do NOT use DETACHED_PROCESS — it breaks the Agent SDK's subprocess I/O.
creation_flags = subprocess.CREATE_NO_WINDOW if sys.platform == "win32" else 0
try:
subprocess.Popen(
cmd,
stdout=subprocess.DEVNULL,
stderr=subprocess.DEVNULL,
creationflags=creation_flags,
)
logging.info("Spawned flush.py for session %s (%d turns, %d chars)", session_id, turn_count, len(context))
except Exception as e:
logging.error("Failed to spawn flush.py: %s", e)
if __name__ == "__main__":
main()

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"""
SessionStart hook - injects knowledge base context into every conversation.
This is the "context injection" layer. When Claude Code starts a session,
this hook reads the knowledge base index and recent daily log, then injects
them as additional context so Claude always "remembers" what it has learned.
Configure in .claude/settings.json:
{
"hooks": {
"SessionStart": [{
"matcher": "",
"command": "uv run python hooks/session-start.py"
}]
}
}
"""
import json
import sys
from datetime import datetime, timedelta, timezone
from pathlib import Path
# Paths relative to project root
ROOT = Path(__file__).resolve().parent.parent
KNOWLEDGE_DIR = ROOT / "knowledge"
DAILY_DIR = ROOT / "daily"
INDEX_FILE = KNOWLEDGE_DIR / "index.md"
MAX_CONTEXT_CHARS = 20_000
MAX_LOG_LINES = 30
def get_recent_log() -> str:
"""Read the most recent daily log (today or yesterday)."""
today = datetime.now(timezone.utc).astimezone()
for offset in range(2):
date = today - timedelta(days=offset)
log_path = DAILY_DIR / f"{date.strftime('%Y-%m-%d')}.md"
if log_path.exists():
lines = log_path.read_text(encoding="utf-8").splitlines()
# Return last N lines to keep context small
recent = lines[-MAX_LOG_LINES:] if len(lines) > MAX_LOG_LINES else lines
return "\n".join(recent)
return "(no recent daily log)"
def build_context() -> str:
"""Assemble the context to inject into the conversation."""
parts = []
# Today's date
today = datetime.now(timezone.utc).astimezone()
parts.append(f"## Today\n{today.strftime('%A, %B %d, %Y')}")
# Knowledge base index (the core retrieval mechanism)
if INDEX_FILE.exists():
index_content = INDEX_FILE.read_text(encoding="utf-8")
parts.append(f"## Knowledge Base Index\n\n{index_content}")
else:
parts.append("## Knowledge Base Index\n\n(empty - no articles compiled yet)")
# Recent daily log
recent_log = get_recent_log()
parts.append(f"## Recent Daily Log\n\n{recent_log}")
context = "\n\n---\n\n".join(parts)
# Truncate if too long
if len(context) > MAX_CONTEXT_CHARS:
context = context[:MAX_CONTEXT_CHARS] + "\n\n...(truncated)"
return context
def main():
context = build_context()
output = {
"hookSpecificOutput": {
"hookEventName": "SessionStart",
"additionalContext": context,
}
}
print(json.dumps(output))
if __name__ == "__main__":
main()

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[project]
name = "llm-personal-kb"
version = "0.1.0"
description = "Personal knowledge base compiled from AI conversations - inspired by Karpathy's LLM KB architecture"
requires-python = ">=3.12"
dependencies = [
"claude-agent-sdk>=0.1.29",
"python-dotenv>=1.0.0",
"tzdata>=2024.1",
]
[tool.ruff]
line-length = 100

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"""
Compile daily conversation logs into structured knowledge articles.
This is the "LLM compiler" - it reads daily logs (source code) and produces
organized knowledge articles (the executable).
Usage:
uv run python compile.py # compile new/changed logs only
uv run python compile.py --all # force recompile everything
uv run python compile.py --file daily/2026-04-01.md # compile a specific log
uv run python compile.py --dry-run # show what would be compiled
"""
from __future__ import annotations
import argparse
import asyncio
import sys
from pathlib import Path
from config import AGENTS_FILE, CONCEPTS_DIR, CONNECTIONS_DIR, DAILY_DIR, KNOWLEDGE_DIR, now_iso
from utils import (
file_hash,
list_raw_files,
list_wiki_articles,
load_state,
read_wiki_index,
save_state,
)
# ── Paths for the LLM to use ──────────────────────────────────────────
ROOT_DIR = Path(__file__).resolve().parent.parent
async def compile_daily_log(log_path: Path, state: dict) -> float:
"""Compile a single daily log into knowledge articles.
Returns the API cost of the compilation.
"""
from claude_agent_sdk import (
AssistantMessage,
ClaudeAgentOptions,
ResultMessage,
TextBlock,
query,
)
log_content = log_path.read_text(encoding="utf-8")
schema = AGENTS_FILE.read_text(encoding="utf-8")
wiki_index = read_wiki_index()
# Read existing articles for context
existing_articles_context = ""
existing = {}
for article_path in list_wiki_articles():
rel = article_path.relative_to(KNOWLEDGE_DIR)
existing[str(rel)] = article_path.read_text(encoding="utf-8")
if existing:
parts = []
for rel_path, content in existing.items():
parts.append(f"### {rel_path}\n```markdown\n{content}\n```")
existing_articles_context = "\n\n".join(parts)
timestamp = now_iso()
prompt = f"""You are a knowledge compiler. Your job is to read a daily conversation log
and extract knowledge into structured wiki articles.
## Schema (AGENTS.md)
{schema}
## Current Wiki Index
{wiki_index}
## Existing Wiki Articles
{existing_articles_context if existing_articles_context else "(No existing articles yet)"}
## Daily Log to Compile
**File:** {log_path.name}
{log_content}
## Your Task
Read the daily log above and compile it into wiki articles following the schema exactly.
### Rules:
1. **Extract key concepts** - Identify 3-7 distinct concepts worth their own article
2. **Create concept articles** in `knowledge/concepts/` - One .md file per concept
- Use the exact article format from AGENTS.md (YAML frontmatter + sections)
- Include `sources:` in frontmatter pointing to the daily log file
- Use `[[concepts/slug]]` wikilinks to link to related concepts
- Write in encyclopedia style - neutral, comprehensive
3. **Create connection articles** in `knowledge/connections/` if this log reveals non-obvious
relationships between 2+ existing concepts
4. **Update existing articles** if this log adds new information to concepts already in the wiki
- Read the existing article, add the new information, add the source to frontmatter
5. **Update knowledge/index.md** - Add new entries to the table
- Each entry: `| [[path/slug]] | One-line summary | source-file | {timestamp[:10]} |`
6. **Append to knowledge/log.md** - Add a timestamped entry:
```
## [{timestamp}] compile | {log_path.name}
- Source: daily/{log_path.name}
- Articles created: [[concepts/x]], [[concepts/y]]
- Articles updated: [[concepts/z]] (if any)
```
### File paths:
- Write concept articles to: {CONCEPTS_DIR}
- Write connection articles to: {CONNECTIONS_DIR}
- Update index at: {KNOWLEDGE_DIR / 'index.md'}
- Append log at: {KNOWLEDGE_DIR / 'log.md'}
### Quality standards:
- Every article must have complete YAML frontmatter
- Every article must link to at least 2 other articles via [[wikilinks]]
- Key Points section should have 3-5 bullet points
- Details section should have 2+ paragraphs
- Related Concepts section should have 2+ entries
- Sources section should cite the daily log with specific claims extracted
"""
cost = 0.0
try:
async for message in query(
prompt=prompt,
options=ClaudeAgentOptions(
cwd=str(ROOT_DIR),
system_prompt={"type": "preset", "preset": "claude_code"},
allowed_tools=["Read", "Write", "Edit", "Glob", "Grep"],
permission_mode="acceptEdits",
max_turns=30,
),
):
if isinstance(message, AssistantMessage):
for block in message.content:
if isinstance(block, TextBlock):
pass # compilation output - LLM writes files directly
elif isinstance(message, ResultMessage):
cost = message.total_cost_usd or 0.0
print(f" Cost: ${cost:.4f}")
except Exception as e:
print(f" Error: {e}")
return 0.0
# Update state
rel_path = log_path.name
state.setdefault("ingested", {})[rel_path] = {
"hash": file_hash(log_path),
"compiled_at": now_iso(),
"cost_usd": cost,
}
state["total_cost"] = state.get("total_cost", 0.0) + cost
save_state(state)
return cost
def main():
parser = argparse.ArgumentParser(description="Compile daily logs into knowledge articles")
parser.add_argument("--all", action="store_true", help="Force recompile all logs")
parser.add_argument("--file", type=str, help="Compile a specific daily log file")
parser.add_argument("--dry-run", action="store_true", help="Show what would be compiled")
args = parser.parse_args()
state = load_state()
# Determine which files to compile
if args.file:
target = Path(args.file)
if not target.is_absolute():
target = DAILY_DIR / target.name
if not target.exists():
# Try resolving relative to project root
target = ROOT_DIR / args.file
if not target.exists():
print(f"Error: {args.file} not found")
sys.exit(1)
to_compile = [target]
else:
all_logs = list_raw_files()
if args.all:
to_compile = all_logs
else:
to_compile = []
for log_path in all_logs:
rel = log_path.name
prev = state.get("ingested", {}).get(rel, {})
if not prev or prev.get("hash") != file_hash(log_path):
to_compile.append(log_path)
if not to_compile:
print("Nothing to compile - all daily logs are up to date.")
return
print(f"{'[DRY RUN] ' if args.dry_run else ''}Files to compile ({len(to_compile)}):")
for f in to_compile:
print(f" - {f.name}")
if args.dry_run:
return
# Compile each file sequentially
total_cost = 0.0
for i, log_path in enumerate(to_compile, 1):
print(f"\n[{i}/{len(to_compile)}] Compiling {log_path.name}...")
cost = asyncio.run(compile_daily_log(log_path, state))
total_cost += cost
print(f" Done.")
articles = list_wiki_articles()
print(f"\nCompilation complete. Total cost: ${total_cost:.2f}")
print(f"Knowledge base: {len(articles)} articles")
if __name__ == "__main__":
main()

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"""Path constants and configuration for the personal knowledge base."""
from pathlib import Path
from datetime import datetime, timezone
# ── Paths ──────────────────────────────────────────────────────────────
ROOT_DIR = Path(__file__).resolve().parent.parent
DAILY_DIR = ROOT_DIR / "daily"
KNOWLEDGE_DIR = ROOT_DIR / "knowledge"
CONCEPTS_DIR = KNOWLEDGE_DIR / "concepts"
CONNECTIONS_DIR = KNOWLEDGE_DIR / "connections"
QA_DIR = KNOWLEDGE_DIR / "qa"
REPORTS_DIR = ROOT_DIR / "reports"
SCRIPTS_DIR = ROOT_DIR / "scripts"
HOOKS_DIR = ROOT_DIR / "hooks"
AGENTS_FILE = ROOT_DIR / "AGENTS.md"
INDEX_FILE = KNOWLEDGE_DIR / "index.md"
LOG_FILE = KNOWLEDGE_DIR / "log.md"
STATE_FILE = SCRIPTS_DIR / "state.json"
# ── Timezone ───────────────────────────────────────────────────────────
TIMEZONE = "America/Chicago"
def now_iso() -> str:
"""Current time in ISO 8601 format."""
return datetime.now(timezone.utc).astimezone().isoformat(timespec="seconds")
def today_iso() -> str:
"""Current date in ISO 8601 format."""
return datetime.now(timezone.utc).astimezone().strftime("%Y-%m-%d")

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"""
Memory flush agent - extracts important knowledge from conversation context.
Spawned by session-end.py or pre-compact.py as a background process. Reads
pre-extracted conversation context from a .md file, uses the Claude Agent SDK
to decide what's worth saving, and appends the result to today's daily log.
Usage:
uv run python flush.py <context_file.md> <session_id>
"""
from __future__ import annotations
# Recursion prevention: set this BEFORE any imports that might trigger Claude
import os
os.environ["CLAUDE_INVOKED_BY"] = "memory_flush"
import asyncio
import json
import logging
import sys
import time
from datetime import datetime, timezone
from pathlib import Path
ROOT = Path(__file__).resolve().parent.parent
DAILY_DIR = ROOT / "daily"
SCRIPTS_DIR = ROOT / "scripts"
STATE_FILE = SCRIPTS_DIR / "last-flush.json"
LOG_FILE = SCRIPTS_DIR / "flush.log"
# Set up file-based logging so we can verify the background process ran.
# The parent process sends stdout/stderr to DEVNULL (to avoid the inherited
# file handle bug on Windows), so this is our only observability channel.
logging.basicConfig(
filename=str(LOG_FILE),
level=logging.INFO,
format="%(asctime)s %(levelname)s %(message)s",
datefmt="%Y-%m-%d %H:%M:%S",
)
def load_flush_state() -> dict:
if STATE_FILE.exists():
try:
return json.loads(STATE_FILE.read_text(encoding="utf-8"))
except (json.JSONDecodeError, OSError):
pass
return {}
def save_flush_state(state: dict) -> None:
STATE_FILE.write_text(json.dumps(state), encoding="utf-8")
def append_to_daily_log(content: str, section: str = "Session") -> None:
"""Append content to today's daily log."""
today = datetime.now(timezone.utc).astimezone()
log_path = DAILY_DIR / f"{today.strftime('%Y-%m-%d')}.md"
if not log_path.exists():
DAILY_DIR.mkdir(parents=True, exist_ok=True)
log_path.write_text(
f"# Daily Log: {today.strftime('%Y-%m-%d')}\n\n## Sessions\n\n## Memory Maintenance\n\n",
encoding="utf-8",
)
time_str = today.strftime("%H:%M")
entry = f"### {section} ({time_str})\n\n{content}\n\n"
with open(log_path, "a", encoding="utf-8") as f:
f.write(entry)
async def run_flush(context: str) -> str:
"""Use Claude Agent SDK to extract important knowledge from conversation context."""
from claude_agent_sdk import (
AssistantMessage,
ClaudeAgentOptions,
ResultMessage,
TextBlock,
query,
)
prompt = f"""Review the conversation context below and respond with a concise summary
of important items that should be preserved in the daily log.
Do NOT use any tools just return plain text.
Format your response as a structured daily log entry with these sections:
**Context:** [One line about what the user was working on]
**Key Exchanges:**
- [Important Q&A or discussions]
**Decisions Made:**
- [Any decisions with rationale]
**Lessons Learned:**
- [Gotchas, patterns, or insights discovered]
**Action Items:**
- [Follow-ups or TODOs mentioned]
Skip anything that is:
- Routine tool calls or file reads
- Content that's trivial or obvious
- Trivial back-and-forth or clarification exchanges
Only include sections that have actual content. If nothing is worth saving,
respond with exactly: FLUSH_OK
## Conversation Context
{context}"""
response = ""
try:
async for message in query(
prompt=prompt,
options=ClaudeAgentOptions(
cwd=str(ROOT),
allowed_tools=[],
max_turns=2,
),
):
if isinstance(message, AssistantMessage):
for block in message.content:
if isinstance(block, TextBlock):
response += block.text
elif isinstance(message, ResultMessage):
pass
except Exception as e:
import traceback
logging.error("Agent SDK error: %s\n%s", e, traceback.format_exc())
response = f"FLUSH_ERROR: {type(e).__name__}: {e}"
return response
COMPILE_AFTER_HOUR = 18 # 6 PM local time
def maybe_trigger_compilation() -> None:
"""If it's past the compile hour and today's log hasn't been compiled, run compile.py."""
import subprocess as _sp
now = datetime.now(timezone.utc).astimezone()
if now.hour < COMPILE_AFTER_HOUR:
return
# Check if today's log has already been compiled
today_log = f"{now.strftime('%Y-%m-%d')}.md"
compile_state_file = SCRIPTS_DIR / "state.json"
if compile_state_file.exists():
try:
compile_state = json.loads(compile_state_file.read_text(encoding="utf-8"))
ingested = compile_state.get("ingested", {})
if today_log in ingested:
# Already compiled today - check if the log has changed since
from hashlib import sha256
log_path = DAILY_DIR / today_log
if log_path.exists():
current_hash = sha256(log_path.read_bytes()).hexdigest()[:16]
if ingested[today_log].get("hash") == current_hash:
return # log unchanged since last compile
except (json.JSONDecodeError, OSError):
pass
compile_script = SCRIPTS_DIR / "compile.py"
if not compile_script.exists():
return
logging.info("End-of-day compilation triggered (after %d:00)", COMPILE_AFTER_HOUR)
cmd = ["uv", "run", "--directory", str(ROOT), "python", str(compile_script)]
kwargs: dict = {}
if sys.platform == "win32":
kwargs["creationflags"] = _sp.CREATE_NEW_PROCESS_GROUP | _sp.DETACHED_PROCESS
else:
kwargs["start_new_session"] = True
try:
log_handle = open(str(SCRIPTS_DIR / "compile.log"), "a")
_sp.Popen(cmd, stdout=log_handle, stderr=_sp.STDOUT, cwd=str(ROOT), **kwargs)
except Exception as e:
logging.error("Failed to spawn compile.py: %s", e)
def main():
if len(sys.argv) < 3:
logging.error("Usage: %s <context_file.md> <session_id>", sys.argv[0])
sys.exit(1)
context_file = Path(sys.argv[1])
session_id = sys.argv[2]
logging.info("flush.py started for session %s, context: %s", session_id, context_file)
if not context_file.exists():
logging.error("Context file not found: %s", context_file)
return
# Deduplication: skip if same session was flushed within 60 seconds
state = load_flush_state()
if (
state.get("session_id") == session_id
and time.time() - state.get("timestamp", 0) < 60
):
logging.info("Skipping duplicate flush for session %s", session_id)
context_file.unlink(missing_ok=True)
return
# Read pre-extracted context
context = context_file.read_text(encoding="utf-8").strip()
if not context:
logging.info("Context file is empty, skipping")
context_file.unlink(missing_ok=True)
return
logging.info("Flushing session %s: %d chars", session_id, len(context))
# Run the LLM extraction
response = asyncio.run(run_flush(context))
# Append to daily log
if "FLUSH_OK" in response:
logging.info("Result: FLUSH_OK")
append_to_daily_log(
"FLUSH_OK - Nothing worth saving from this session", "Memory Flush"
)
elif "FLUSH_ERROR" in response:
logging.error("Result: %s", response)
append_to_daily_log(response, "Memory Flush")
else:
logging.info("Result: saved to daily log (%d chars)", len(response))
append_to_daily_log(response, "Session")
# Update dedup state
save_flush_state({"session_id": session_id, "timestamp": time.time()})
# Clean up context file
context_file.unlink(missing_ok=True)
# End-of-day auto-compilation: if it's past the compile hour and today's
# log hasn't been compiled yet, trigger compile.py in the background.
maybe_trigger_compilation()
logging.info("Flush complete for session %s", session_id)
if __name__ == "__main__":
main()

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"""
Lint the knowledge base for structural and semantic health.
Runs 7 checks: broken links, orphan pages, orphan sources, stale articles,
contradictions (LLM), missing backlinks, and sparse articles.
Usage:
uv run python lint.py # all checks
uv run python lint.py --structural-only # skip LLM checks (faster, cheaper)
"""
from __future__ import annotations
import argparse
import asyncio
from pathlib import Path
from config import KNOWLEDGE_DIR, REPORTS_DIR, now_iso, today_iso
from utils import (
count_inbound_links,
extract_wikilinks,
file_hash,
get_article_word_count,
list_raw_files,
list_wiki_articles,
load_state,
read_all_wiki_content,
save_state,
wiki_article_exists,
)
ROOT_DIR = Path(__file__).resolve().parent.parent
def check_broken_links() -> list[dict]:
"""Check for [[wikilinks]] that point to non-existent articles."""
issues = []
for article in list_wiki_articles():
content = article.read_text(encoding="utf-8")
rel = article.relative_to(KNOWLEDGE_DIR)
for link in extract_wikilinks(content):
if link.startswith("daily/"):
continue # daily log references are valid
if not wiki_article_exists(link):
issues.append({
"severity": "error",
"check": "broken_link",
"file": str(rel),
"detail": f"Broken link: [[{link}]] - target does not exist",
})
return issues
def check_orphan_pages() -> list[dict]:
"""Check for articles with zero inbound links."""
issues = []
for article in list_wiki_articles():
rel = article.relative_to(KNOWLEDGE_DIR)
link_target = str(rel).replace(".md", "").replace("\\", "/")
inbound = count_inbound_links(link_target)
if inbound == 0:
issues.append({
"severity": "warning",
"check": "orphan_page",
"file": str(rel),
"detail": f"Orphan page: no other articles link to [[{link_target}]]",
})
return issues
def check_orphan_sources() -> list[dict]:
"""Check for daily logs that haven't been compiled yet."""
state = load_state()
ingested = state.get("ingested", {})
issues = []
for log_path in list_raw_files():
if log_path.name not in ingested:
issues.append({
"severity": "warning",
"check": "orphan_source",
"file": f"daily/{log_path.name}",
"detail": f"Uncompiled daily log: {log_path.name} has not been ingested",
})
return issues
def check_stale_articles() -> list[dict]:
"""Check if source daily logs have changed since compilation."""
state = load_state()
ingested = state.get("ingested", {})
issues = []
for log_path in list_raw_files():
rel = log_path.name
if rel in ingested:
stored_hash = ingested[rel].get("hash", "")
current_hash = file_hash(log_path)
if stored_hash != current_hash:
issues.append({
"severity": "warning",
"check": "stale_article",
"file": f"daily/{rel}",
"detail": f"Stale: {rel} has changed since last compilation",
})
return issues
def check_missing_backlinks() -> list[dict]:
"""Check for asymmetric links: A links to B but B doesn't link to A."""
issues = []
for article in list_wiki_articles():
content = article.read_text(encoding="utf-8")
rel = article.relative_to(KNOWLEDGE_DIR)
source_link = str(rel).replace(".md", "").replace("\\", "/")
for link in extract_wikilinks(content):
if link.startswith("daily/"):
continue
target_path = KNOWLEDGE_DIR / f"{link}.md"
if target_path.exists():
target_content = target_path.read_text(encoding="utf-8")
if f"[[{source_link}]]" not in target_content:
issues.append({
"severity": "suggestion",
"check": "missing_backlink",
"file": str(rel),
"detail": f"[[{source_link}]] links to [[{link}]] but not vice versa",
"auto_fixable": True,
})
return issues
def check_sparse_articles() -> list[dict]:
"""Check for articles with fewer than 200 words."""
issues = []
for article in list_wiki_articles():
word_count = get_article_word_count(article)
if word_count < 200:
rel = article.relative_to(KNOWLEDGE_DIR)
issues.append({
"severity": "suggestion",
"check": "sparse_article",
"file": str(rel),
"detail": f"Sparse article: {word_count} words (minimum recommended: 200)",
})
return issues
async def check_contradictions() -> list[dict]:
"""Use LLM to detect contradictions across articles."""
from claude_agent_sdk import (
AssistantMessage,
ClaudeAgentOptions,
ResultMessage,
TextBlock,
query,
)
wiki_content = read_all_wiki_content()
prompt = f"""Review this knowledge base for contradictions, inconsistencies, or
conflicting claims across articles.
## Knowledge Base
{wiki_content}
## Instructions
Look for:
- Direct contradictions (article A says X, article B says not-X)
- Inconsistent recommendations (different articles recommend conflicting approaches)
- Outdated information that conflicts with newer entries
For each issue found, output EXACTLY one line in this format:
CONTRADICTION: [file1] vs [file2] - description of the conflict
INCONSISTENCY: [file] - description of the inconsistency
If no issues found, output exactly: NO_ISSUES
Do NOT output anything else - no preamble, no explanation, just the formatted lines."""
response = ""
try:
async for message in query(
prompt=prompt,
options=ClaudeAgentOptions(
cwd=str(ROOT_DIR),
allowed_tools=[],
max_turns=2,
),
):
if isinstance(message, AssistantMessage):
for block in message.content:
if isinstance(block, TextBlock):
response += block.text
except Exception as e:
return [{"severity": "error", "check": "contradiction", "file": "(system)", "detail": f"LLM check failed: {e}"}]
issues = []
if "NO_ISSUES" not in response:
for line in response.strip().split("\n"):
line = line.strip()
if line.startswith("CONTRADICTION:") or line.startswith("INCONSISTENCY:"):
issues.append({
"severity": "warning",
"check": "contradiction",
"file": "(cross-article)",
"detail": line,
})
return issues
def generate_report(all_issues: list[dict]) -> str:
"""Generate a markdown lint report."""
errors = [i for i in all_issues if i["severity"] == "error"]
warnings = [i for i in all_issues if i["severity"] == "warning"]
suggestions = [i for i in all_issues if i["severity"] == "suggestion"]
lines = [
f"# Lint Report - {today_iso()}",
"",
f"**Total issues:** {len(all_issues)}",
f"- Errors: {len(errors)}",
f"- Warnings: {len(warnings)}",
f"- Suggestions: {len(suggestions)}",
"",
]
for severity, issues, marker in [
("Errors", errors, "x"),
("Warnings", warnings, "!"),
("Suggestions", suggestions, "?"),
]:
if issues:
lines.append(f"## {severity}")
lines.append("")
for issue in issues:
fixable = " (auto-fixable)" if issue.get("auto_fixable") else ""
lines.append(f"- **[{marker}]** `{issue['file']}` - {issue['detail']}{fixable}")
lines.append("")
if not all_issues:
lines.append("All checks passed. Knowledge base is healthy.")
lines.append("")
return "\n".join(lines)
def main():
parser = argparse.ArgumentParser(description="Lint the knowledge base")
parser.add_argument(
"--structural-only",
action="store_true",
help="Skip LLM-based checks (contradictions) - faster and free",
)
args = parser.parse_args()
print("Running knowledge base lint checks...")
all_issues: list[dict] = []
# Structural checks (free, instant)
checks = [
("Broken links", check_broken_links),
("Orphan pages", check_orphan_pages),
("Orphan sources", check_orphan_sources),
("Stale articles", check_stale_articles),
("Missing backlinks", check_missing_backlinks),
("Sparse articles", check_sparse_articles),
]
for name, check_fn in checks:
print(f" Checking: {name}...")
issues = check_fn()
all_issues.extend(issues)
print(f" Found {len(issues)} issue(s)")
# LLM check (costs money)
if not args.structural_only:
print(" Checking: Contradictions (LLM)...")
issues = asyncio.run(check_contradictions())
all_issues.extend(issues)
print(f" Found {len(issues)} issue(s)")
else:
print(" Skipping: Contradictions (--structural-only)")
# Generate and save report
report = generate_report(all_issues)
REPORTS_DIR.mkdir(parents=True, exist_ok=True)
report_path = REPORTS_DIR / f"lint-{today_iso()}.md"
report_path.write_text(report, encoding="utf-8")
print(f"\nReport saved to: {report_path}")
# Update state
state = load_state()
state["last_lint"] = now_iso()
save_state(state)
# Summary
errors = sum(1 for i in all_issues if i["severity"] == "error")
warnings = sum(1 for i in all_issues if i["severity"] == "warning")
suggestions = sum(1 for i in all_issues if i["severity"] == "suggestion")
print(f"\nResults: {errors} errors, {warnings} warnings, {suggestions} suggestions")
if errors > 0:
print("\nErrors found - knowledge base needs attention!")
return 1
return 0
if __name__ == "__main__":
exit(main())

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"""
Query the knowledge base using index-guided retrieval (no RAG).
The LLM reads the index, picks relevant articles, and synthesizes an answer.
No vector database, no embeddings, no chunking - just structured markdown
and an index the LLM can reason over.
Usage:
uv run python query.py "How should I handle auth redirects?"
uv run python query.py "What patterns do I use for API design?" --file-back
"""
from __future__ import annotations
import argparse
import asyncio
from pathlib import Path
from config import KNOWLEDGE_DIR, QA_DIR, now_iso
from utils import load_state, read_all_wiki_content, save_state
ROOT_DIR = Path(__file__).resolve().parent.parent
async def run_query(question: str, file_back: bool = False) -> str:
"""Query the knowledge base and optionally file the answer back."""
from claude_agent_sdk import (
AssistantMessage,
ClaudeAgentOptions,
ResultMessage,
TextBlock,
query,
)
wiki_content = read_all_wiki_content()
tools = ["Read", "Glob", "Grep"]
if file_back:
tools.extend(["Write", "Edit"])
file_back_instructions = ""
if file_back:
timestamp = now_iso()
file_back_instructions = f"""
## File Back Instructions
After answering, do the following:
1. Create a Q&A article at {QA_DIR}/ with the filename being a slugified version
of the question (e.g., knowledge/qa/how-to-handle-auth-redirects.md)
2. Use the Q&A article format from the schema (frontmatter with title, question,
consulted articles, filed date)
3. Update {KNOWLEDGE_DIR / 'index.md'} with a new row for this Q&A article
4. Append to {KNOWLEDGE_DIR / 'log.md'}:
## [{timestamp}] query (filed) | question summary
- Question: {question}
- Consulted: [[list of articles read]]
- Filed to: [[qa/article-name]]
"""
prompt = f"""You are a knowledge base query engine. Answer the user's question by
consulting the knowledge base below.
## How to Answer
1. Read the INDEX section first - it lists every article with a one-line summary
2. Identify 3-10 articles that are relevant to the question
3. Read those articles carefully (they're included below)
4. Synthesize a clear, thorough answer
5. Cite your sources using [[wikilinks]] (e.g., [[concepts/supabase-auth]])
6. If the knowledge base doesn't contain relevant information, say so honestly
## Knowledge Base
{wiki_content}
## Question
{question}
{file_back_instructions}"""
answer = ""
cost = 0.0
try:
async for message in query(
prompt=prompt,
options=ClaudeAgentOptions(
cwd=str(ROOT_DIR),
system_prompt={"type": "preset", "preset": "claude_code"},
allowed_tools=tools,
permission_mode="acceptEdits",
max_turns=15,
),
):
if isinstance(message, AssistantMessage):
for block in message.content:
if isinstance(block, TextBlock):
answer += block.text
elif isinstance(message, ResultMessage):
cost = message.total_cost_usd or 0.0
except Exception as e:
answer = f"Error querying knowledge base: {e}"
# Update state
state = load_state()
state["query_count"] = state.get("query_count", 0) + 1
state["total_cost"] = state.get("total_cost", 0.0) + cost
save_state(state)
return answer
def main():
parser = argparse.ArgumentParser(description="Query the personal knowledge base")
parser.add_argument("question", help="The question to ask")
parser.add_argument(
"--file-back",
action="store_true",
help="File the answer back into the knowledge base as a Q&A article",
)
args = parser.parse_args()
print(f"Question: {args.question}")
print(f"File back: {'yes' if args.file_back else 'no'}")
print("-" * 60)
answer = asyncio.run(run_query(args.question, file_back=args.file_back))
print(answer)
if args.file_back:
print("\n" + "-" * 60)
qa_count = len(list(QA_DIR.glob("*.md"))) if QA_DIR.exists() else 0
print(f"Answer filed to knowledge/qa/ ({qa_count} Q&A articles total)")
if __name__ == "__main__":
main()

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"""Shared utilities for the personal knowledge base."""
import hashlib
import json
import re
from pathlib import Path
from config import (
CONCEPTS_DIR,
CONNECTIONS_DIR,
DAILY_DIR,
INDEX_FILE,
KNOWLEDGE_DIR,
LOG_FILE,
QA_DIR,
STATE_FILE,
)
# ── State management ──────────────────────────────────────────────────
def load_state() -> dict:
"""Load persistent state from state.json."""
if STATE_FILE.exists():
return json.loads(STATE_FILE.read_text(encoding="utf-8"))
return {"ingested": {}, "query_count": 0, "last_lint": None, "total_cost": 0.0}
def save_state(state: dict) -> None:
"""Save state to state.json."""
STATE_FILE.write_text(json.dumps(state, indent=2), encoding="utf-8")
# ── File hashing ──────────────────────────────────────────────────────
def file_hash(path: Path) -> str:
"""SHA-256 hash of a file (first 16 hex chars)."""
return hashlib.sha256(path.read_bytes()).hexdigest()[:16]
# ── Slug / naming ─────────────────────────────────────────────────────
def slugify(text: str) -> str:
"""Convert text to a filename-safe slug."""
text = text.lower().strip()
text = re.sub(r"[^\w\s-]", "", text)
text = re.sub(r"[\s_]+", "-", text)
text = re.sub(r"-+", "-", text)
return text.strip("-")
# ── Wikilink helpers ──────────────────────────────────────────────────
def extract_wikilinks(content: str) -> list[str]:
"""Extract all [[wikilinks]] from markdown content."""
return re.findall(r"\[\[([^\]]+)\]\]", content)
def wiki_article_exists(link: str) -> bool:
"""Check if a wikilinked article exists on disk."""
path = KNOWLEDGE_DIR / f"{link}.md"
return path.exists()
# ── Wiki content helpers ──────────────────────────────────────────────
def read_wiki_index() -> str:
"""Read the knowledge base index file."""
if INDEX_FILE.exists():
return INDEX_FILE.read_text(encoding="utf-8")
return "# Knowledge Base Index\n\n| Article | Summary | Compiled From | Updated |\n|---------|---------|---------------|---------|"
def read_all_wiki_content() -> str:
"""Read index + all wiki articles into a single string for context."""
parts = [f"## INDEX\n\n{read_wiki_index()}"]
for subdir in [CONCEPTS_DIR, CONNECTIONS_DIR, QA_DIR]:
if not subdir.exists():
continue
for md_file in sorted(subdir.glob("*.md")):
rel = md_file.relative_to(KNOWLEDGE_DIR)
content = md_file.read_text(encoding="utf-8")
parts.append(f"## {rel}\n\n{content}")
return "\n\n---\n\n".join(parts)
def list_wiki_articles() -> list[Path]:
"""List all wiki article files."""
articles = []
for subdir in [CONCEPTS_DIR, CONNECTIONS_DIR, QA_DIR]:
if subdir.exists():
articles.extend(sorted(subdir.glob("*.md")))
return articles
def list_raw_files() -> list[Path]:
"""List all daily log files."""
if not DAILY_DIR.exists():
return []
return sorted(DAILY_DIR.glob("*.md"))
# ── Index helpers ─────────────────────────────────────────────────────
def count_inbound_links(target: str, exclude_file: Path | None = None) -> int:
"""Count how many wiki articles link to a given target."""
count = 0
for article in list_wiki_articles():
if article == exclude_file:
continue
content = article.read_text(encoding="utf-8")
if f"[[{target}]]" in content:
count += 1
return count
def get_article_word_count(path: Path) -> int:
"""Count words in an article, excluding YAML frontmatter."""
content = path.read_text(encoding="utf-8")
# Strip frontmatter
if content.startswith("---"):
end = content.find("---", 3)
if end != -1:
content = content[end + 3:]
return len(content.split())
def build_index_entry(rel_path: str, summary: str, sources: str, updated: str) -> str:
"""Build a single index table row."""
link = rel_path.replace(".md", "")
return f"| [[{link}]] | {summary} | {sources} | {updated} |"

636
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@ -0,0 +1,636 @@
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