Anto01 1a8fdf4225 fix: chroma restore bind-mount bug + consolidate docs
Two fixes from the 2026-04-09 first real restore drill on Dalidou,
plus the long-overdue doc consolidation I should have done when I
added the drill runbook instead of creating a duplicate.

## Chroma restore bind-mount bug (drill finding)

src/atocore/ops/backup.py: restore_runtime_backup() used to call
shutil.rmtree(dst_chroma) before copying the snapshot back. In the
Dockerized Dalidou deployment the chroma dir is a bind-mounted
volume — you can't unlink a mount point, rmtree raises
  OSError [Errno 16] Device or resource busy
and the restore silently fails to touch Chroma. This bit the first
real drill; the operator worked around it with --no-chroma plus a
manual cp -a.

Fix: clear the destination's CONTENTS (iterdir + rmtree/unlink per
child) and use copytree(dirs_exist_ok=True) so the mount point
itself is never touched. Equivalent semantics, bind-mount-safe.

Regression test:
tests/test_backup.py::test_restore_chroma_does_not_unlink_destination_directory
captures Path.stat().st_ino of the dest dir before and after
restore and asserts they match. That's the same invariant a
bind-mounted chroma dir enforces — if the inode changed, the
mount would have failed. 11/11 backup tests now pass.

## Doc consolidation

docs/backup-restore-drill.md existed as a duplicate of the
authoritative docs/backup-restore-procedure.md. When I added the
drill runbook in commit 3362080 I wrote it from scratch instead of
updating the existing procedure — bad doc hygiene on a project
that's literally about being a context engine.

- Deleted docs/backup-restore-drill.md
- Folded its contents into docs/backup-restore-procedure.md:
  - Replaced the manual sudo cp restore sequence with the new
    `python -m atocore.ops.backup restore <STAMP>
    --confirm-service-stopped` CLI
  - Added the one-shot docker compose run pattern for running
    restore inside a container that reuses the live volume mounts
  - Documented the --no-pre-snapshot / --no-chroma / --chroma flags
  - New "Chroma restore and bind-mounted volumes" subsection
    explaining the bug and the regression test that protects the fix
  - New "Restore drill" subsection with three levels (unit tests,
    module round-trip, live Dalidou drill) and the cadence list
  - Failure-mode table gained four entries: restored_integrity_ok,
    Device-or-resource-busy, drill marker still present,
    chroma_snapshot_missing
  - "Open follow-ups" struck the restore_runtime_backup item (done)
    and added a "Done (historical)" note referencing 2026-04-09
  - Quickstart cheat sheet now has a full drill one-liner using
    memory_type=episodic (the 2026-04-09 drill found the runbook's
    memory_type=note was invalid — the valid set is identity,
    preference, project, episodic, knowledge, adaptation)

## Status doc sync

Long overdue — I've been landing code without updating the
project's narrative state docs.

docs/current-state.md:
- "Reliability Baseline" now reflects: restore_runtime_backup is
  real with CLI, pre-restore safety snapshot, WAL cleanup,
  integrity check; live drill on 2026-04-09 surfaced and fixed
  Chroma bind-mount bug; deploy provenance via /health build_sha;
  deploy.sh self-update re-exec guard
- "Immediate Next Focus" reshuffled: drill re-run (priority 1) and
  auto-capture (priority 2) are now ahead of retrieval quality work,
  reflecting the updated unblock sequence

docs/next-steps.md:
- New item 1: re-run the drill with chroma working end-to-end
- New item 2: auto-capture conservative mode (Stop hook)
- Old item 7 rewritten as item 9 listing what's DONE
  (create/list/validate/restore, admin/backup endpoint with
  include_chroma, /health provenance, self-update guard,
  procedure doc with failure modes) and what's still pending
  (retention cleanup, off-Dalidou target, auto-validation)

## Test count

226 passing (was 225 + 1 new inode-stability regression test).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
2026-04-09 09:13:21 -04:00

AtoCore

Personal context engine that enriches LLM interactions with durable memory, structured context, and project knowledge.

Quick Start

pip install -e .
uvicorn src.atocore.main:app --port 8100

Usage

# Ingest markdown files
curl -X POST http://localhost:8100/ingest \
  -H "Content-Type: application/json" \
  -d '{"path": "/path/to/notes"}'

# Build enriched context for a prompt
curl -X POST http://localhost:8100/context/build \
  -H "Content-Type: application/json" \
  -d '{"prompt": "What is the project status?", "project": "myproject"}'

# CLI ingestion
python scripts/ingest_folder.py --path /path/to/notes

# Live operator client
python scripts/atocore_client.py health
python scripts/atocore_client.py audit-query "gigabit" 5

API Endpoints

Method Path Description
POST /ingest Ingest markdown file or folder
POST /query Retrieve relevant chunks
POST /context/build Build full context pack
GET /health Health check
GET /debug/context Inspect last context pack

Architecture

FastAPI (port 8100)
  |- Ingestion: markdown -> parse -> chunk -> embed -> store
  |- Retrieval: query -> embed -> vector search -> rank
  |- Context Builder: retrieve -> boost -> budget -> format
  |- SQLite (documents, chunks, memories, projects, interactions)
  '- ChromaDB (vector embeddings)

Configuration

Set via environment variables (prefix ATOCORE_):

Variable Default Description
ATOCORE_DEBUG false Enable debug logging
ATOCORE_PORT 8100 Server port
ATOCORE_CHUNK_MAX_SIZE 800 Max chunk size (chars)
ATOCORE_CONTEXT_BUDGET 3000 Context pack budget (chars)
ATOCORE_EMBEDDING_MODEL paraphrase-multilingual-MiniLM-L12-v2 Embedding model

Testing

pip install -e ".[dev]"
pytest

Operations

  • scripts/atocore_client.py provides a live API client for project refresh, project-state inspection, and retrieval-quality audits.
  • docs/operations.md captures the current operational priority order: retrieval quality, Wave 2 trusted-operational ingestion, AtoDrive scoping, and restore validation.

Architecture Notes

Implementation-facing architecture notes live under docs/architecture/.

Current additions:

  • docs/architecture/engineering-knowledge-hybrid-architecture.md — 5-layer hybrid model
  • docs/architecture/engineering-ontology-v1.md — V1 object and relationship inventory
  • docs/architecture/engineering-query-catalog.md — 20 v1-required queries
  • docs/architecture/memory-vs-entities.md — canonical home split
  • docs/architecture/promotion-rules.md — Layer 0 to Layer 2 pipeline
  • docs/architecture/conflict-model.md — contradictory facts detection and resolution
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