fix: route legacy-usearch notices to stderr for clean structured output

docs/LLM_CLI_INTEGRATION.md

@@ -145,6 +145,6 @@ sia-code search "AuthService"
 - Prefer MCP when the client supports it; it removes the need to distribute prompt-side workflow files.
 - `engineering_bootstrap` is the intended portable first-call surface for engineering workflows when users only add `uvx sia-code-mcp` to their MCP config.
 - Keep the skill file short and practical for fallback environments.
-- `memory git-context` is currently CLI-first for file history + blast radius workflows.
+- Use `memory git-context` in CLI workflows or `git_context` through MCP.
 - Update this file when CLI behavior changes.
 - Keep both PyPI and local-checkout workflows documented during active development.

docs/MCP_INTEGRATION.md

@@ -48,6 +48,7 @@ Exposed in v1:
 - `memory_export`, `memory_import`
 - `config_show`, `config_path`, `config_get`, `config_set`
 - `embed_start`, `embed_status`, `embed_stop`
+- `git_context`
 
 ## Recommended First Call
 
@@ -61,7 +62,6 @@ For engineering work in Claude Code, OpenCode, Codex, or any MCP-aware client, p
 
 Not exposed in v1:
 
-- `memory git-context` (CLI-only today for file history + blast radius)
 - interactive CLI mode
 - watch mode indexing
 - config editor launching

sia_code/cli.py

@@ -23,7 +23,12 @@
 from .config import Config
 from .indexer.coordinator import IndexingCoordinator
 
-console = Console(force_terminal=True)
+console = Console(
+    force_terminal=True, color_system="auto" if sys.stdout.isatty() else None
+)
+err_console = Console(
+    stderr=True, force_terminal=True, color_system="auto" if sys.stderr.isatty() else None
+)
 
 
 def _display_skip_summary(
@@ -139,11 +144,11 @@ def create_backend(
     )
     if is_implicit_sqlite_default_on_legacy_usearch:
         if not suppress_stdout_notices:
-            console.print(
+            err_console.print(
                 "[yellow]Detected legacy usearch index with implicit storage backend.[/yellow] "
                 "Using legacy backend for compatibility."
             )
-            console.print(
+            err_console.print(
                 "[dim]Set 'storage.backend=sqlite-vec' and run 'sia-code index --clean .' "
                 "to migrate when ready.[/dim]"
             )
@@ -167,10 +172,10 @@ def create_backend(
 
     if effective_backend == "auto" and detected_backend == "usearch":
         if not suppress_stdout_notices:
-            console.print(
+            err_console.print(
                 "[yellow]Detected legacy usearch index.[/yellow] Using it for compatibility."
             )
-            console.print(
+            err_console.print(
                 "[dim]Set 'storage.backend=usearch' to pin legacy mode, "
                 "or run 'sia-code index --clean .' to migrate to sqlite-vec.[/dim]"
             )
@@ -2969,15 +2974,14 @@ def memory_git_context(file_paths, no_blast_radius, no_narrative, output_format)
         sia-code memory git-context src/api.py src/crud.py --format json
         sia-code memory git-context src/api.py --no-narrative
     """
-    from .config import Config
     from .memory.blast_radius import BlastRadiusAnalyzer
     from .memory.diff_analyzer import DiffSemanticAnalyzer
     from .memory.git_dynamic import GitDynamicMemory
     from .memory.intent_classifier import IntentClassifier
     from .memory.recency import RecencyConfig
 
     project_dir = Path.cwd()
-    config = Config.load(project_dir / ".sia-code" / "config.json")
+    _, config = require_initialized()
     gc = config.git_dynamic
 
     recency_cfg = RecencyConfig(

sia_code/mcp.py

@@ -834,7 +834,7 @@ def engineering_bootstrap(
                 hit_files = list({m["file_path"] for m in search_hits["matches"] if "file_path" in m})[:3]
                 if hit_files:
                     git_context_payload = _compute_git_context(
-                        context.workspace_root, hit_files, limit=3
+                        context.workspace_root, config, hit_files, limit=3
                     )
         except Exception:
             pass  # Graceful — git context is supplementary
@@ -1109,8 +1109,11 @@ def memory_trace(
         try:
             if result.related_files:
                 dynamic_git = _compute_git_context(
-                    context.workspace_root, result.related_files[:3],
-                    limit=3, include_blast_radius=False,
+                    context.workspace_root,
+                    config,
+                    result.related_files[:3],
+                    limit=3,
+                    include_blast_radius=False,
                 )
         except Exception:
             pass
@@ -1284,23 +1287,19 @@ def embed_stop():
 
     def _compute_git_context(
         workspace_root: Path,
+        config: Config,
         file_paths: list[str],
         limit: int = 5,
         include_blast_radius: bool = True,
         include_narrative: bool = True,
     ) -> dict:
-        """Shared helper — computes git context for files.
-
-        Used by git_context tool, research, engineering_bootstrap, memory_trace.
-        """
-        from .config import Config
+        """Shared helper — computes git context for files."""
         from .memory.blast_radius import BlastRadiusAnalyzer
         from .memory.diff_analyzer import DiffSemanticAnalyzer
         from .memory.git_dynamic import GitDynamicMemory
         from .memory.intent_classifier import IntentClassifier
         from .memory.recency import RecencyConfig
 
-        config = Config.load(workspace_root / ".sia-code" / "config.json")
         gc = config.git_dynamic
 
         if not gc.enabled:
@@ -1401,6 +1400,7 @@ def _compute_git_context(
     def git_context(
         workspace_root: str,
         file_paths: list[str],
+        index_dir: str | None = None,
         include_blast_radius: bool = True,
         include_narrative: bool = True,
     ) -> dict:
@@ -1410,13 +1410,15 @@ def git_context(
         co-change blast radius, and model-generated evolution narrative.
         Auto-uses local flan-t5 model for narrative when available.
         """
+        context, config = _require_initialized_context(workspace_root, index_dir)
         result = _compute_git_context(
-            Path(workspace_root),
+            context.workspace_root,
+            config,
             file_paths,
             include_blast_radius=include_blast_radius,
             include_narrative=include_narrative,
         )
-        return _ok(scope="project", result=result)
+        return _ok(context=context, result=result)
 
     return mcp
 

sia_code/runtime_context.py

@@ -14,6 +14,7 @@
 from .config import Config
 
 console = Console()
+err_console = Console(stderr=True)
 
 
 @dataclass(frozen=True)
@@ -46,11 +47,11 @@ def create_backend(
     )
     if is_implicit_sqlite_default_on_legacy_usearch:
         if not suppress_stdout_notices:
-            console.print(
+            err_console.print(
                 "[yellow]Detected legacy usearch index with implicit storage backend.[/yellow] "
                 "Using legacy backend for compatibility."
             )
-            console.print(
+            err_console.print(
                 "[dim]Set 'storage.backend=sqlite-vec' and run 'sia-code index --clean .' "
                 "to migrate when ready.[/dim]"
             )
@@ -74,10 +75,10 @@ def create_backend(
 
     if effective_backend == "auto" and detected_backend == "usearch":
         if not suppress_stdout_notices:
-            console.print(
+            err_console.print(
                 "[yellow]Detected legacy usearch index.[/yellow] Using it for compatibility."
             )
-            console.print(
+            err_console.print(
                 "[dim]Set 'storage.backend=usearch' to pin legacy mode, "
                 "or run 'sia-code index --clean .' to migrate to sqlite-vec.[/dim]"
             )

skills/sia-code/SKILL.md

@@ -67,7 +67,7 @@ uvx sia-code memory working-set "auth flow" \
 ```
 
 - `memory working-set` emits stable JSON for agent handoff.
-- `memory git-context` is CLI-only and useful before risky refactors.
+- `memory git-context` is useful before risky refactors; MCP clients use `git_context`.
 
 ## Multi-Repo and Worktrees
 

tests/integration/test_git_dynamic_real_repos.py

@@ -12,7 +12,6 @@
 from sia_code.memory.git_dynamic import GitDynamicMemory
 from sia_code.memory.blast_radius import BlastRadiusAnalyzer
 from sia_code.memory.recency import RecencyConfig, RecencyScorer
-from sia_code.memory.revert_detector import RevertDetector, CommitInfo
 from sia_code.memory.intent_classifier import IntentClassifier
 
 
@@ -145,7 +144,6 @@ def test_within_window_full_weight(self):
 
     def test_halflife_gives_half_weight(self):
         from datetime import datetime, timedelta, timezone
-        import math
 
         scorer = RecencyScorer(RecencyConfig(halflife_days=30, working_window_days=14))
         now = datetime.now(timezone.utc)

tests/unit/test_cli_backend_selection.py

@@ -92,3 +92,31 @@ def fake_create_backend(
 
     assert result.exit_code == 0
     assert captured["suppress_stdout_notices"] is True
+
+
+def test_git_context_command_uses_resolved_index(monkeypatch, tmp_path):
+    resolved = False
+
+    def fake_require_initialized():
+        nonlocal resolved
+        resolved = True
+        return tmp_path / "custom-index", Config()
+
+    monkeypatch.chdir(tmp_path)
+    monkeypatch.setattr("sia_code.cli.require_initialized", fake_require_initialized)
+
+    result = CliRunner().invoke(
+        main,
+        [
+            "memory",
+            "git-context",
+            "missing.py",
+            "--no-blast-radius",
+            "--no-narrative",
+            "--format",
+            "json",
+        ],
+    )
+
+    assert result.exit_code == 0, result.output
+    assert resolved is True

tests/unit/test_index_dir_resolution.py

@@ -1,5 +1,3 @@
-from pathlib import Path
-
 import pytest
 
 from sia_code.cli import resolve_index_dir

tests/unit/test_mcp_lock.py

@@ -1,5 +1,3 @@
-from pathlib import Path
-
 from sia_code.mcp_lock import index_lock, lock_path_for_index
 
 

tests/unit/test_mcp_server.py

@@ -46,10 +46,62 @@ async def test_build_server_registers_expected_tool_names():
     server = build_server()
     tool_names = {tool.name for tool in await server.list_tools()}
 
-    assert {"init", "status", "search", "research"}.issubset(tool_names)
-    assert {"memory_working_set", "config_show", "embed_status"}.issubset(tool_names)
-    assert {"health_check", "engineering_bootstrap"}.issubset(tool_names)
-    assert "interactive" not in tool_names
+    assert tool_names == {
+        "compact",
+        "config_get",
+        "config_path",
+        "config_set",
+        "config_show",
+        "embed_start",
+        "embed_status",
+        "embed_stop",
+        "engineering_bootstrap",
+        "git_context",
+        "health_check",
+        "index",
+        "init",
+        "memory_add_decision",
+        "memory_approve",
+        "memory_changelog",
+        "memory_export",
+        "memory_import",
+        "memory_list",
+        "memory_reject",
+        "memory_search",
+        "memory_sync_git",
+        "memory_timeline",
+        "memory_trace",
+        "memory_working_set",
+        "research",
+        "search",
+        "status",
+    }
+
+
+@pytest.mark.anyio
+async def test_git_context_uses_explicit_index_dir(tmp_path):
+    workspace_root = tmp_path / "repo"
+    workspace_root.mkdir()
+    index_dir = tmp_path / "custom-index"
+    index_dir.mkdir()
+    Config().save(index_dir / "config.json")
+
+    server = build_server()
+    result = decode_tool_result(
+        await server.call_tool(
+            "git_context",
+            {
+                "workspace_root": str(workspace_root),
+                "index_dir": str(index_dir),
+                "file_paths": ["missing.py"],
+                "include_blast_radius": False,
+                "include_narrative": False,
+            },
+        )
+    )
+
+    assert result["ok"] is True
+    assert result["resolved_index_dir"] == str(index_dir.resolve())
 
 
 @pytest.mark.anyio

tests/unit/test_multi_hop.py

@@ -506,12 +506,11 @@ def test_uses_hybrid_variants_when_budgeted_embeddings_enabled(self, backend, sa
         backend.embedding_enabled = True
         backend.embedding_granularity = "budget"
 
-        original_search_hybrid = backend.search_hybrid
         calls = []
 
         def mock_search_hybrid(query, *args, **kwargs):
             calls.append(query)
-            return original_search_hybrid(query, *args, **kwargs)
+            return []
 
         backend.search_hybrid = mock_search_hybrid
 

tests/unit/test_open_index_writable.py

@@ -36,7 +36,16 @@ def __len__(self):
         def ndim(self):
             return 768
 
-    monkeypatch.setattr(usearch_backend, "Index", FakeIndex)
+    class FakeMetricKind:
+        Cos = "cos"
+        L2sq = "l2sq"
+
+    monkeypatch.setattr(
+        usearch_backend, "_lazy_usearch", lambda: (FakeIndex, FakeMetricKind)
+    )
+    monkeypatch.setattr(
+        usearch_backend.UsearchSqliteBackend, "_get_embedder", lambda self: None
+    )
 
     backend = usearch_backend.UsearchSqliteBackend(path=tmp_path)
     backend.open_index(writable=True)