feat: implement AtoCore Phase 0 + Phase 0.5 (foundation + PoC)

Complete implementation of the personal context engine foundation:
- FastAPI server with 5 endpoints (ingest, query, context/build, health, debug)
- SQLite database with 5 tables (documents, chunks, memories, projects, interactions)
- Heading-aware markdown chunker (800 char max, recursive splitting)
- Multilingual embeddings via sentence-transformers (EN/FR)
- ChromaDB vector store with cosine similarity retrieval
- Context builder with project boosting, dedup, and budget enforcement
- CLI scripts for batch ingestion and test prompt evaluation
- 19 unit tests passing, 79% coverage
- Validated on 482 real project files (8383 chunks, 0 errors)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/atocore/models/database.py

@@ -0,0 +1,98 @@
+"""SQLite database schema and connection management."""
+
+import sqlite3
+from contextlib import contextmanager
+from pathlib import Path
+from typing import Generator
+
+from atocore.config import settings
+from atocore.observability.logger import get_logger
+
+log = get_logger("database")
+
+SCHEMA_SQL = """
+CREATE TABLE IF NOT EXISTS source_documents (
+    id TEXT PRIMARY KEY,
+    file_path TEXT UNIQUE NOT NULL,
+    file_hash TEXT NOT NULL,
+    title TEXT,
+    doc_type TEXT DEFAULT 'markdown',
+    tags TEXT DEFAULT '[]',
+    ingested_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+    updated_at DATETIME DEFAULT CURRENT_TIMESTAMP
+);
+
+CREATE TABLE IF NOT EXISTS source_chunks (
+    id TEXT PRIMARY KEY,
+    document_id TEXT NOT NULL REFERENCES source_documents(id) ON DELETE CASCADE,
+    chunk_index INTEGER NOT NULL,
+    content TEXT NOT NULL,
+    heading_path TEXT DEFAULT '',
+    char_count INTEGER NOT NULL,
+    metadata TEXT DEFAULT '{}',
+    created_at DATETIME DEFAULT CURRENT_TIMESTAMP
+);
+
+CREATE TABLE IF NOT EXISTS memories (
+    id TEXT PRIMARY KEY,
+    memory_type TEXT NOT NULL,
+    content TEXT NOT NULL,
+    source_chunk_id TEXT REFERENCES source_chunks(id),
+    confidence REAL DEFAULT 1.0,
+    status TEXT DEFAULT 'active',
+    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+    updated_at DATETIME DEFAULT CURRENT_TIMESTAMP
+);
+
+CREATE TABLE IF NOT EXISTS projects (
+    id TEXT PRIMARY KEY,
+    name TEXT UNIQUE NOT NULL,
+    description TEXT DEFAULT '',
+    status TEXT DEFAULT 'active',
+    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+    updated_at DATETIME DEFAULT CURRENT_TIMESTAMP
+);
+
+CREATE TABLE IF NOT EXISTS interactions (
+    id TEXT PRIMARY KEY,
+    prompt TEXT NOT NULL,
+    context_pack TEXT DEFAULT '{}',
+    response_summary TEXT DEFAULT '',
+    project_id TEXT REFERENCES projects(id),
+    created_at DATETIME DEFAULT CURRENT_TIMESTAMP
+);
+
+CREATE INDEX IF NOT EXISTS idx_chunks_document ON source_chunks(document_id);
+CREATE INDEX IF NOT EXISTS idx_memories_type ON memories(memory_type);
+CREATE INDEX IF NOT EXISTS idx_memories_status ON memories(status);
+CREATE INDEX IF NOT EXISTS idx_interactions_project ON interactions(project_id);
+"""
+
+
+def _ensure_data_dir() -> None:
+    settings.data_dir.mkdir(parents=True, exist_ok=True)
+
+
+def init_db() -> None:
+    """Initialize the database with schema."""
+    _ensure_data_dir()
+    with get_connection() as conn:
+        conn.executescript(SCHEMA_SQL)
+    log.info("database_initialized", path=str(settings.db_path))
+
+
+@contextmanager
+def get_connection() -> Generator[sqlite3.Connection, None, None]:
+    """Get a database connection with row factory."""
+    _ensure_data_dir()
+    conn = sqlite3.connect(str(settings.db_path))
+    conn.row_factory = sqlite3.Row
+    conn.execute("PRAGMA foreign_keys = ON")
+    try:
+        yield conn
+        conn.commit()
+    except Exception:
+        conn.rollback()
+        raise
+    finally:
+        conn.close()