Stabilize chunk upserts, attach git commit context to memory, and stabilize tests

README.md

@@ -112,6 +112,19 @@ sia-code index --clean
 
 View config: `sia-code config show`
 
+**Git worktrees:** by default, sia-code auto-detects worktrees and stores a single shared index in the git common dir. You can override with `SIA_CODE_INDEX_SCOPE` or set an explicit path with `SIA_CODE_INDEX_DIR`.
+
+```bash
+# Force shared index even outside worktrees
+export SIA_CODE_INDEX_SCOPE=shared
+
+# Or disable auto-detection (per-worktree index)
+export SIA_CODE_INDEX_SCOPE=worktree
+
+sia-code init
+sia-code index .
+```
+
 **AI Summarization** (optional, enhances git changelogs):
 
 ```json

docs/CLI_FEATURES.md

@@ -79,6 +79,13 @@ sia-code init [OPTIONS]
 | `--path PATH` | Directory to initialize | `.` (current directory) |
 | `--dry-run` | Preview project analysis without creating index | `false` |
 
+**Environment variables:**
+
+| Variable | Description |
+|----------|-------------|
+| `SIA_CODE_INDEX_DIR` | Override the index directory (absolute or project-relative) |
+| `SIA_CODE_INDEX_SCOPE` | Set to `shared` to reuse one index across git worktrees |
+
 **Examples:**
 
 ```bash
@@ -100,7 +107,7 @@ sia-code init --dry-run
    - Finds documentation files
    - Determines recommended search strategy
 
-2. **Creates `.sia-code/` directory:**
+2. **Creates index directory:**
    - `config.json` - Configuration with auto-detected settings
    - `vectors.usearch` - HNSW vector index (created empty)
    - `index.db` - SQLite database with FTS5 (created empty)

docs/MEMORY_FEATURES.md

@@ -9,6 +9,7 @@ Memory features help teams:
 - **Understand history** - What changed and when?
 - **Share context** - Export/import decisions across teams
 - **Maintain documentation** - Auto-generate from git history
+- **Preserve timing** - Record commit hashes/timestamps for traceability
 
 ## Features
 
@@ -57,6 +58,8 @@ Auto-extracted from git commit history.
 - Breaking changes
 - Major refactors
 
+Each event stores the source commit hash and timestamp for auditability.
+
 **Example:**
 ```python
 # Auto-extracted from git log

sia_code/cli.py

@@ -1,7 +1,10 @@
 """CLI entry point for Sia Code."""
 
+import os
 import sys
 import logging
+import subprocess
+from datetime import datetime
 from pathlib import Path
 
 import click
@@ -128,6 +131,117 @@ def create_backend(index_path: Path, config: Config, valid_chunks=None):
     )
 
 
+def resolve_git_common_dir(base_dir: Path) -> Path | None:
+    """Return git common dir path if available for a repository."""
+    try:
+        result = subprocess.run(
+            ["git", "rev-parse", "--git-common-dir"],
+            cwd=base_dir,
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+    except (OSError, subprocess.CalledProcessError):
+        return None
+
+    output = result.stdout.strip()
+    if not output:
+        return None
+
+    common_dir = Path(output)
+    if not common_dir.is_absolute():
+        common_dir = (base_dir / common_dir).resolve()
+    return common_dir
+
+
+def is_git_worktree(base_dir: Path) -> bool:
+    """Return True when base_dir is inside a git worktree.
+
+    In a normal repo, `--git-dir` and `--git-common-dir` resolve to the same path.
+    In a linked worktree, the worktree's git dir differs from the common dir.
+    """
+
+    try:
+        git_dir_result = subprocess.run(
+            ["git", "rev-parse", "--git-dir"],
+            cwd=base_dir,
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+        common_dir_result = subprocess.run(
+            ["git", "rev-parse", "--git-common-dir"],
+            cwd=base_dir,
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+    except (OSError, subprocess.CalledProcessError):
+        return False
+
+    git_dir_raw = git_dir_result.stdout.strip()
+    common_dir_raw = common_dir_result.stdout.strip()
+    if not git_dir_raw or not common_dir_raw:
+        return False
+
+    git_dir = Path(git_dir_raw)
+    if not git_dir.is_absolute():
+        git_dir = (base_dir / git_dir).resolve()
+
+    common_dir = Path(common_dir_raw)
+    if not common_dir.is_absolute():
+        common_dir = (base_dir / common_dir).resolve()
+
+    return git_dir != common_dir
+
+
+def get_git_commit_context(base_dir: Path) -> tuple[str | None, datetime | None]:
+    """Return the current git commit hash and commit time for a directory."""
+    try:
+        commit_result = subprocess.run(
+            ["git", "rev-parse", "HEAD"],
+            cwd=base_dir,
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+        time_result = subprocess.run(
+            ["git", "show", "-s", "--format=%cI", "HEAD"],
+            cwd=base_dir,
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+    except (OSError, subprocess.CalledProcessError):
+        return None, None
+
+    commit_hash = commit_result.stdout.strip() or None
+    commit_time_raw = time_result.stdout.strip()
+    commit_time = datetime.fromisoformat(commit_time_raw) if commit_time_raw else None
+    return commit_hash, commit_time
+
+
+def resolve_index_dir(project_dir: Path | None = None) -> Path:
+    """Resolve the index directory, honoring environment overrides."""
+    base_dir = project_dir or Path(".")
+    override = os.environ.get("SIA_CODE_INDEX_DIR")
+    if override:
+        override_path = Path(override)
+        if override_path.is_absolute():
+            return override_path
+        return base_dir / override_path
+
+    scope = os.environ.get("SIA_CODE_INDEX_SCOPE")
+    if not scope or scope == "auto":
+        scope = "shared" if is_git_worktree(base_dir) else "worktree"
+    if scope == "shared":
+        common_dir = resolve_git_common_dir(base_dir)
+        if common_dir is not None:
+            return common_dir / "sia-code"
+
+    return base_dir / ".sia-code"
+
+
 def require_initialized() -> tuple[Path, Config]:
     """Ensure Sia Code is initialized, return sia_dir and config.
 
@@ -137,7 +251,7 @@ def require_initialized() -> tuple[Path, Config]:
     Raises:
         SystemExit: If .sia-code directory doesn't exist
     """
-    sia_dir = Path(".sia-code")
+    sia_dir = resolve_index_dir()
     if not sia_dir.exists():
         console.print("[red]Error: Sia Code not initialized. Run 'sia-code init' first.[/red]")
         sys.exit(1)
@@ -164,7 +278,7 @@ def init(path: str, dry_run: bool):
     from .indexer.project_analyzer import ProjectAnalyzer
 
     project_dir = Path(path)
-    sia_dir = project_dir / ".sia-code"
+    sia_dir = resolve_index_dir(project_dir)
 
     if sia_dir.exists() and not dry_run:
         console.print(f"[yellow]Sia Code already initialized at {sia_dir}[/yellow]")
@@ -190,7 +304,7 @@ def init(path: str, dry_run: bool):
         console.print("\n[yellow]Dry run complete. No index created.[/yellow]")
         return
 
-    # Create .sia-code directory
+    # Create index directory
     sia_dir.mkdir(parents=True, exist_ok=True)
     (sia_dir / "cache").mkdir(exist_ok=True)
 
@@ -1413,12 +1527,16 @@ def memory_add_decision(title, description, reasoning, alternatives):
 
         session_id = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
 
+        commit_hash, commit_time = get_git_commit_context(Path("."))
+
         decision_id = backend.add_decision(
             session_id=session_id,
             title=title,
             description=description,
             reasoning=reasoning,
             alternatives=alt_list,
+            commit_hash=commit_hash,
+            commit_time=commit_time,
         )
 
         console.print(f"[green]✓[/green] Created decision #{decision_id}: {title}")
@@ -1821,9 +1939,7 @@ def memory_changelog(range, output_format, output):
 
 
 @memory.command(name="export")
-@click.option(
-    "-o", "--output", type=click.Path(), default=".sia-code/memory.json", help="Output file"
-)
+@click.option("-o", "--output", type=click.Path(), default=None, help="Output file")
 def memory_export(output):
     """Export memory to JSON file.
 
@@ -1834,6 +1950,8 @@ def memory_export(output):
     backend.open_index()
 
     try:
+        if output is None:
+            output = str(sia_dir / "memory.json")
         export_path = backend.export_memory(include_pending=True)
 
         # Copy to specified output location if different
@@ -1855,7 +1973,7 @@ def memory_export(output):
     "--input",
     "input_file",
     type=click.Path(exists=True),
-    default=".sia-code/memory.json",
+    default=None,
     help="Input file",
 )
 def memory_import(input_file):
@@ -1868,6 +1986,8 @@ def memory_import(input_file):
     backend.open_index(writable=True)
 
     try:
+        if input_file is None:
+            input_file = str(sia_dir / "memory.json")
         result = backend.import_memory(input_file)
 
         console.print("[green]✓[/green] Import complete")

sia_code/core/models.py

@@ -166,6 +166,8 @@ class Decision:
     alternatives: list[dict[str, Any]] = field(default_factory=list)
     status: str = "pending"  # 'pending', 'approved', 'rejected'
     category: str | None = None  # Set when approved
+    commit_hash: str | None = None
+    commit_time: datetime | None = None
     created_at: datetime | None = None
     approved_at: datetime | None = None
 
@@ -180,6 +182,8 @@ def to_dict(self) -> dict[str, Any]:
             "alternatives": self.alternatives,
             "status": self.status,
             "category": self.category,
+            "commit_hash": self.commit_hash,
+            "commit_time": self.commit_time.isoformat() if self.commit_time else None,
             "created_at": self.created_at.isoformat() if self.created_at else None,
             "approved_at": self.approved_at.isoformat() if self.approved_at else None,
         }
@@ -197,6 +201,8 @@ class TimelineEvent:
     files_changed: list[str] = field(default_factory=list)
     diff_stats: dict[str, Any] = field(default_factory=dict)
     importance: str = "medium"  # 'high', 'medium', 'low'
+    commit_hash: str | None = None
+    commit_time: datetime | None = None
     created_at: datetime | None = None
 
     def to_dict(self) -> dict[str, Any]:
@@ -210,6 +216,8 @@ def to_dict(self) -> dict[str, Any]:
             "files_changed": self.files_changed,
             "diff_stats": self.diff_stats,
             "importance": self.importance,
+            "commit_hash": self.commit_hash,
+            "commit_time": self.commit_time.isoformat() if self.commit_time else None,
             "created_at": self.created_at.isoformat() if self.created_at else None,
         }
 
@@ -226,6 +234,8 @@ class ChangelogEntry:
     breaking_changes: list[str] = field(default_factory=list)
     features: list[str] = field(default_factory=list)
     fixes: list[str] = field(default_factory=list)
+    commit_hash: str | None = None
+    commit_time: datetime | None = None
     created_at: datetime | None = None
 
     def to_dict(self) -> dict[str, Any]:
@@ -239,6 +249,8 @@ def to_dict(self) -> dict[str, Any]:
             "breaking_changes": self.breaking_changes,
             "features": self.features,
             "fixes": self.fixes,
+            "commit_hash": self.commit_hash,
+            "commit_time": self.commit_time.isoformat() if self.commit_time else None,
             "created_at": self.created_at.isoformat() if self.created_at else None,
         }