codegraph-engine 2.1.8__tar.gz → 2.2.0__tar.gz

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: codegraph-engine
-Version: 2.1.8
+Version: 2.2.0
 Summary: Deep deterministic repository intelligence for AI coding agents (code, dependencies, databases, and runtime observations)
 Author: CodeGraph contributors
 License-Expression: MIT
@@ -35,24 +35,24 @@ Dynamic: license-file
   <img src="docs/assets/codegraph_logo.jpg" alt="CodeGraph MCP — Deep Deterministic Repository Intelligence for AI Coding Agents" width="500" />
 </p>
 
-<h1 align="center">CodeGraph Engine (v2.1.8)</h1>
+<h1 align="center">CodeGraph-MCP Engine (v2.2.0)</h1>
 
 <p align="center">
   <strong>Deep deterministic repository intelligence for AI coding agents.</strong>
 </p>
 
 <p align="center">
-  <a href="https://pypi.org/project/codegraph-engine/2.1.8/"><img src="https://img.shields.io/badge/pypi-codegraph--engine%20v2.1.8-blue.svg" alt="PyPI: codegraph-engine v2.1.8" /></a>
+  <a href="https://pypi.org/project/codegraph-engine/2.2.0/"><img src="https://img.shields.io/badge/pypi-codegraph--engine%20v2.2.0-blue.svg" alt="PyPI: codegraph-engine v2.2.0" /></a>
   <a href="pyproject.toml"><img src="https://img.shields.io/badge/python-3.12%20%7C%203.13-3776AB.svg" alt="Python 3.12 | 3.13" /></a>
   <a href="src/codegraph/mcp/server.py"><img src="https://img.shields.io/badge/MCP-14%20default%20%7C%2056%20full%20tools-2ea043.svg" alt="MCP Tools: 14 default | 56 full" /></a>
-  <a href="tests/"><img src="https://img.shields.io/badge/pytest-853%20passed-brightgreen.svg" alt="Tests: 853 passed" /></a>
+  <a href="tests/"><img src="https://img.shields.io/badge/pytest-861%20passed-brightgreen.svg" alt="Tests: 861 passed" /></a>
   <a href="pyproject.toml"><img src="https://img.shields.io/badge/ruff-0%20errors-success.svg" alt="Ruff: 0 errors" /></a>
-  <a href="src/codegraph/"><img src="https://img.shields.io/badge/mypy-0%20issues%20(79%20files)-blue.svg" alt="Mypy: strict" /></a>
+  <a href="src/codegraph/"><img src="https://img.shields.io/badge/mypy-0%20issues%20(80%20files)-blue.svg" alt="Mypy: strict" /></a>
   <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License: MIT" /></a>
 </p>
 
 <p align="center">
-  <a href="https://pypi.org/project/codegraph-engine/2.1.8/"><strong>PyPI (v2.1.8)</strong></a> •
+  <a href="https://pypi.org/project/codegraph-engine/2.2.0/"><strong>PyPI (v2.2.0)</strong></a> •
   <a href="#2-quickstart-30-second-setup"><strong>Quickstart</strong></a> •
   <a href="#1-built-for-aiml-and-backend-heavy-repositories"><strong>Built For</strong></a> •
   <a href="#5-database-intelligence"><strong>Database Intelligence</strong></a> •
@@ -126,7 +126,7 @@ pip install "codegraph-engine[mcp]"
 
 ### Step 2: Configure Your AI Coding Agents (`codegraph install`)
 
-CodeGraph includes an interactive, idempotent onboarding installer ([`src/codegraph/installer.py`](src/codegraph/installer.py)) that detects installed AI coding agents (**Claude Code**, **Cursor**, **Antigravity**, **Codex CLI**, **Gemini CLI**, and **Cline**), configures `mcpServers.codegraph`, installs marker-bounded routing instructions (`<!-- CODEGRAPH:START -->` … `<!-- CODEGRAPH:END -->`), and verifies MCP server startup:
+CodeGraph-MCP includes an interactive, idempotent onboarding installer ([`src/codegraph/installer.py`](src/codegraph/installer.py)) that detects installed AI coding agents (**Claude Code**, **Cursor**, **Antigravity**, **Codex CLI**, **Gemini CLI**, and **Cline**), configures `mcpServers.codegraph`, installs marker-bounded routing instructions (`<!-- CODEGRAPH:START -->` … `<!-- CODEGRAPH:END -->`), and verifies MCP server startup:
 
 ```bash
 # Interactive setup (detects installed agents, previews planned changes, asks confirmation)
@@ -232,7 +232,7 @@ InferenceService.run_inference
                                    db:table:postgresql.public.prediction_logs
 ```
 
-**What CodeGraph structurally proves**:
+**What CodeGraph-MCP structurally proves**:
 - `find_routes(path="/v1/predict")` resolves composed router prefixes (`MOUNTS`) to `predict_endpoint`.
 - `trace_path(from_symbol="predict_endpoint", to_symbol="log_prediction")` proves the multi-hop execution chain across DI injection, preprocessing, model execution, and persistence.
 - `get_db_impact(symbol="InferenceService.run_inference")` identifies downstream writes to `prediction_logs`.
@@ -250,7 +250,7 @@ TrainingPipeline.run
       └──►CALLS (AST_VERIFIED) ──► Evaluator.compute_metrics
 ```
 
-**What CodeGraph structurally proves**:
+**What CodeGraph-MCP structurally proves**:
 - `find_callees(symbol="TrainingPipeline.run")` enumerates every stage of the pipeline with exact file and line ranges.
 - `find_tests(symbol="Evaluator.compute_metrics")` locates the unit and regression tests covering metric calculation.
 - When a transform or model class is dynamically instantiated from a YAML string (`getattr(models, cfg.arch)`), CodeGraph explicitly records `POSSIBLE_CALLS` (`POSSIBLE`) or `UNRESOLVED_REFERENCE` (`UNKNOWN`) rather than fabricating a false static call edge.
@@ -269,7 +269,7 @@ AgentRunner.execute_step
       └──►CALLS (AST_VERIFIED)           ──► ModelProviderClient.generate
 ```
 
-**What CodeGraph structurally proves**:
+**What CodeGraph-MCP structurally proves**:
 - Tracks decorator and call-based registrations (`@tool_registry.register("search_orders")`) via `REGISTERS` and `REGISTERED_HANDLER` edges.
 - Tracks environment variable dependencies (`os.getenv("OPENAI_API_KEY")`) as `READS_ENV` edges with the variable name only—never indexing or exposing secret values.
 

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/README.md

@@ -2,24 +2,24 @@
   <img src="docs/assets/codegraph_logo.jpg" alt="CodeGraph MCP — Deep Deterministic Repository Intelligence for AI Coding Agents" width="500" />
 </p>
 
-<h1 align="center">CodeGraph Engine (v2.1.8)</h1>
+<h1 align="center">CodeGraph-MCP Engine (v2.2.0)</h1>
 
 <p align="center">
   <strong>Deep deterministic repository intelligence for AI coding agents.</strong>
 </p>
 
 <p align="center">
-  <a href="https://pypi.org/project/codegraph-engine/2.1.8/"><img src="https://img.shields.io/badge/pypi-codegraph--engine%20v2.1.8-blue.svg" alt="PyPI: codegraph-engine v2.1.8" /></a>
+  <a href="https://pypi.org/project/codegraph-engine/2.2.0/"><img src="https://img.shields.io/badge/pypi-codegraph--engine%20v2.2.0-blue.svg" alt="PyPI: codegraph-engine v2.2.0" /></a>
   <a href="pyproject.toml"><img src="https://img.shields.io/badge/python-3.12%20%7C%203.13-3776AB.svg" alt="Python 3.12 | 3.13" /></a>
   <a href="src/codegraph/mcp/server.py"><img src="https://img.shields.io/badge/MCP-14%20default%20%7C%2056%20full%20tools-2ea043.svg" alt="MCP Tools: 14 default | 56 full" /></a>
-  <a href="tests/"><img src="https://img.shields.io/badge/pytest-853%20passed-brightgreen.svg" alt="Tests: 853 passed" /></a>
+  <a href="tests/"><img src="https://img.shields.io/badge/pytest-861%20passed-brightgreen.svg" alt="Tests: 861 passed" /></a>
   <a href="pyproject.toml"><img src="https://img.shields.io/badge/ruff-0%20errors-success.svg" alt="Ruff: 0 errors" /></a>
-  <a href="src/codegraph/"><img src="https://img.shields.io/badge/mypy-0%20issues%20(79%20files)-blue.svg" alt="Mypy: strict" /></a>
+  <a href="src/codegraph/"><img src="https://img.shields.io/badge/mypy-0%20issues%20(80%20files)-blue.svg" alt="Mypy: strict" /></a>
   <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License: MIT" /></a>
 </p>
 
 <p align="center">
-  <a href="https://pypi.org/project/codegraph-engine/2.1.8/"><strong>PyPI (v2.1.8)</strong></a> •
+  <a href="https://pypi.org/project/codegraph-engine/2.2.0/"><strong>PyPI (v2.2.0)</strong></a> •
   <a href="#2-quickstart-30-second-setup"><strong>Quickstart</strong></a> •
   <a href="#1-built-for-aiml-and-backend-heavy-repositories"><strong>Built For</strong></a> •
   <a href="#5-database-intelligence"><strong>Database Intelligence</strong></a> •
@@ -93,7 +93,7 @@ pip install "codegraph-engine[mcp]"
 
 ### Step 2: Configure Your AI Coding Agents (`codegraph install`)
 
-CodeGraph includes an interactive, idempotent onboarding installer ([`src/codegraph/installer.py`](src/codegraph/installer.py)) that detects installed AI coding agents (**Claude Code**, **Cursor**, **Antigravity**, **Codex CLI**, **Gemini CLI**, and **Cline**), configures `mcpServers.codegraph`, installs marker-bounded routing instructions (`<!-- CODEGRAPH:START -->` … `<!-- CODEGRAPH:END -->`), and verifies MCP server startup:
+CodeGraph-MCP includes an interactive, idempotent onboarding installer ([`src/codegraph/installer.py`](src/codegraph/installer.py)) that detects installed AI coding agents (**Claude Code**, **Cursor**, **Antigravity**, **Codex CLI**, **Gemini CLI**, and **Cline**), configures `mcpServers.codegraph`, installs marker-bounded routing instructions (`<!-- CODEGRAPH:START -->` … `<!-- CODEGRAPH:END -->`), and verifies MCP server startup:
 
 ```bash
 # Interactive setup (detects installed agents, previews planned changes, asks confirmation)
@@ -199,7 +199,7 @@ InferenceService.run_inference
                                    db:table:postgresql.public.prediction_logs
 ```
 
-**What CodeGraph structurally proves**:
+**What CodeGraph-MCP structurally proves**:
 - `find_routes(path="/v1/predict")` resolves composed router prefixes (`MOUNTS`) to `predict_endpoint`.
 - `trace_path(from_symbol="predict_endpoint", to_symbol="log_prediction")` proves the multi-hop execution chain across DI injection, preprocessing, model execution, and persistence.
 - `get_db_impact(symbol="InferenceService.run_inference")` identifies downstream writes to `prediction_logs`.
@@ -217,7 +217,7 @@ TrainingPipeline.run
       └──►CALLS (AST_VERIFIED) ──► Evaluator.compute_metrics
 ```
 
-**What CodeGraph structurally proves**:
+**What CodeGraph-MCP structurally proves**:
 - `find_callees(symbol="TrainingPipeline.run")` enumerates every stage of the pipeline with exact file and line ranges.
 - `find_tests(symbol="Evaluator.compute_metrics")` locates the unit and regression tests covering metric calculation.
 - When a transform or model class is dynamically instantiated from a YAML string (`getattr(models, cfg.arch)`), CodeGraph explicitly records `POSSIBLE_CALLS` (`POSSIBLE`) or `UNRESOLVED_REFERENCE` (`UNKNOWN`) rather than fabricating a false static call edge.
@@ -236,7 +236,7 @@ AgentRunner.execute_step
       └──►CALLS (AST_VERIFIED)           ──► ModelProviderClient.generate
 ```
 
-**What CodeGraph structurally proves**:
+**What CodeGraph-MCP structurally proves**:
 - Tracks decorator and call-based registrations (`@tool_registry.register("search_orders")`) via `REGISTERS` and `REGISTERED_HANDLER` edges.
 - Tracks environment variable dependencies (`os.getenv("OPENAI_API_KEY")`) as `READS_ENV` edges with the variable name only—never indexing or exposing secret values.
 

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "codegraph-engine"
-version = "2.1.8"
+version = "2.2.0"
 description = "Deep deterministic repository intelligence for AI coding agents (code, dependencies, databases, and runtime observations)"
 readme = "README.md"
 requires-python = ">=3.12"

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/src/codegraph/__init__.py

@@ -1,6 +1,6 @@
 """CodeGraph MCP: local, evidence-backed codebase intelligence."""
 
-__version__ = "2.1.8"
+__version__ = "2.2.0"
 from codegraph.errors import (
     CodeGraphError,
     ErrorCode,

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/src/codegraph/cli.py

@@ -434,6 +434,8 @@ def routes(
     framework: Annotated[str | None, typer.Option("--framework", "-f", help="Filter by framework (e.g. flask, fastapi)")] = None,
     method: Annotated[str | None, typer.Option("--method", "-m", help="Filter by HTTP method (e.g. GET, POST)")] = None,
     route_path: Annotated[str | None, typer.Option("--path", "-p", help="Filter by route path substring")] = None,
+    limit: Annotated[int | None, typer.Option("--limit", "-l", help="Maximum number of routes to return")] = None,
+    offset: Annotated[int, typer.Option("--offset", help="Number of routes to skip")] = 0,
     json_output: Annotated[bool, typer.Option("--json", help="Output raw JSON array")] = False,
 ) -> None:
     """List and inspect indexed framework routes."""
@@ -479,6 +481,11 @@ def routes(
             for r in rows
         ]
 
+        if limit is not None:
+            safe_offset = max(0, offset)
+            safe_limit = max(0, limit)
+            route_list = route_list[safe_offset : safe_offset + safe_limit]
+
         if json_output:
             typer.echo(json.dumps(route_list, indent=2))
         else:
@@ -597,19 +604,60 @@ def debug(
         )
 
 
-@app.command()
-def serve(
-    path: Annotated[Path | None, typer.Argument(help="Repository path (default: current directory)")] = None,
+@app.command(
+    "run",
+    context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
+)
+def run_cmd(
+    ctx: typer.Context,
+    command: Annotated[list[str] | None, typer.Argument(help="Development command and arguments to execute")] = None,
     repository: Annotated[Path | None, typer.Option("--repository", "-r", "--repo", help="Repository path")] = None,
-    profile: Annotated[str, typer.Option("--profile", help="Tool profile: core | minimal | developer | full")] = "full",
+    sample_rate: Annotated[float, typer.Option("--sample-rate", help="Sampling rate for trace capture (0.0..1.0)")] = 1.0,
+) -> None:
+    """Execute a development command or server with transparent runtime trace capture."""
+    full_cmd = (command or []) + ctx.args
+    if not full_cmd:
+        cli_echo("Error: Command cannot be empty. Usage: codegraph run <command> [args...]")
+        raise typer.Exit(code=1)
+
+    repo = _resolve_repo(None, repository)
+    from codegraph.runtime.runner import run_with_telemetry
+
+    exit_code = run_with_telemetry(full_cmd, repository=repo, sample_rate=sample_rate)
+    raise typer.Exit(code=exit_code)
+
+
+def _run_server(
+    path: Path | None,
+    repository: Path | None,
+    profile: str,
+    transport: str = "stdio",
+    host: str = "127.0.0.1",
+    port: int = 8765,
 ) -> None:
-    """Run the stdio MCP server (requires the optional mcp extra)."""
     repo = _resolve_repo(path, repository)
     from codegraph.mcp import create_server
     from codegraph.process_lifecycle import run_mcp_stdio_server
 
-    server = create_server(repo, profile=profile)
-    run_mcp_stdio_server(server, repo, profile=profile)
+    if transport.lower() == "sse":
+        server = create_server(repo, profile=profile, host=host, port=port)
+        server.run(transport="sse")
+    else:
+        server = create_server(repo, profile=profile)
+        run_mcp_stdio_server(server, repo, profile=profile)
+
+
+@app.command()
+def serve(
+    path: Annotated[Path | None, typer.Argument(help="Repository path (default: current directory)")] = None,
+    repository: Annotated[Path | None, typer.Option("--repository", "-r", "--repo", help="Repository path")] = None,
+    profile: Annotated[str, typer.Option("--profile", help="Tool profile: core | minimal | developer | full")] = "full",
+    transport: Annotated[str, typer.Option("--transport", "-t", help="MCP transport: stdio | sse")] = "stdio",
+    host: Annotated[str, typer.Option("--host", help="Host for SSE server")] = "127.0.0.1",
+    port: Annotated[int, typer.Option("--port", "-p", help="Port for SSE server")] = 8765,
+) -> None:
+    """Run the CodeGraph MCP server via stdio or SSE transport."""
+    _run_server(path, repository, profile, transport=transport, host=host, port=port)
 
 
 mcp_app = typer.Typer(help="MCP server commands.")
@@ -621,14 +669,12 @@ def mcp_serve(
     path: Annotated[Path | None, typer.Argument(help="Repository path (default: current directory)")] = None,
     repository: Annotated[Path | None, typer.Option("--repository", "-r", "--repo", help="Repository path")] = None,
     profile: Annotated[str, typer.Option("--profile", help="Tool profile: core | graph | minimal | developer | full")] = "full",
+    transport: Annotated[str, typer.Option("--transport", "-t", help="MCP transport: stdio | sse")] = "stdio",
+    host: Annotated[str, typer.Option("--host", help="Host for SSE server")] = "127.0.0.1",
+    port: Annotated[int, typer.Option("--port", "-p", help="Port for SSE server")] = 8765,
 ) -> None:
-    """Run the stdio MCP server (requires the optional mcp extra)."""
-    repo = _resolve_repo(path, repository)
-    from codegraph.mcp import create_server
-    from codegraph.process_lifecycle import run_mcp_stdio_server
-
-    server = create_server(repo, profile=profile)
-    run_mcp_stdio_server(server, repo, profile=profile)
+    """Run the CodeGraph MCP server via stdio or SSE transport."""
+    _run_server(path, repository, profile, transport=transport, host=host, port=port)
 
 
 def _execute_stop(

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/src/codegraph/context.py

@@ -594,6 +594,7 @@ def _get_context_impl(
             if path:
                 c = sqlite3.connect(f"file:{path}?mode=ro", uri=True)
                 c.row_factory = sqlite3.Row
+                c.execute("PRAGMA busy_timeout = 15000")
                 try:
                     for query in queries:
                         for item in search(
@@ -629,6 +630,7 @@ def _get_context_impl(
                 if path:
                     c = sqlite3.connect(f"file:{path}?mode=ro", uri=True)
                     c.row_factory = sqlite3.Row
+                    c.execute("PRAGMA busy_timeout = 15000")
                     try:
                         return c.execute(
                             "SELECT route_path, http_method, handler_name, file_path, line, endpoint_id FROM framework_routes"
@@ -665,6 +667,7 @@ def _get_context_impl(
                 if path:
                     c = sqlite3.connect(f"file:{path}?mode=ro", uri=True)
                     c.row_factory = sqlite3.Row
+                    c.execute("PRAGMA busy_timeout = 15000")
                     try:
                         archs.append(get_architecture(c, repo))
                     finally:

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/src/codegraph/database/interrogation.py

@@ -748,6 +748,8 @@ def get_db_schema(
     schema: str | None = None,
     *,
     dialect: str | None = None,
+    limit: int | None = None,
+    offset: int = 0,
 ) -> dict[str, Any]:
     """Return the complete repository database schema overview with safe credential redaction."""
     if isinstance(repo_or_dialect, str) and not dialect:
@@ -800,21 +802,42 @@ def get_db_schema(
 
     dialects = sorted({t["dialect"] for t in tables if t.get("dialect")}) or ["UNKNOWN"]
 
-    return redact_payload({
+    safe_tables = tables
+    safe_models = models
+    safe_migrations = migrations
+    safe_cols = columns
+    safe_rels = rels
+
+    if limit is not None:
+        safe_offset = max(0, offset)
+        safe_limit = max(0, limit)
+        safe_tables = tables[safe_offset : safe_offset + safe_limit]
+        safe_models = models[safe_offset : safe_offset + safe_limit]
+        safe_migrations = migrations[safe_offset : safe_offset + safe_limit]
+        safe_cols = columns[: max(safe_limit * 5, 20)]
+        safe_rels = rels[: max(safe_limit * 5, 20)]
+
+    result_dict: dict[str, Any] = {
         "status": "ok",
         "dialects": dialects,
         "table_count": len(tables),
         "column_count": len(columns),
         "model_count": len(models),
         "migration_count": len(migrations),
-        "tables": tables,
-        "columns": columns,
-        "models": models,
-        "relationships": rels,
-        "migrations": migrations,
+        "tables": safe_tables,
+        "columns": safe_cols,
+        "models": safe_models,
+        "relationships": safe_rels,
+        "migrations": safe_migrations,
         "env_variables": env_vars,
         "database_credentials": "REDACTED",
-    })
+    }
+    if limit is not None:
+        result_dict["limit"] = safe_limit
+        result_dict["offset"] = safe_offset
+        result_dict["has_more"] = (safe_offset + len(safe_tables)) < len(tables)
+
+    return redact_payload(result_dict)
 
 
 def get_db_impact(

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/src/codegraph/freshness.py

@@ -235,30 +235,68 @@ def check_freshness(
     deleted: list[str] = []
     parse_failed: list[str] = []
 
-    try:
-        rows = con.execute("SELECT path, hash, status FROM files").fetchall()
-    except sqlite3.OperationalError:
-        rows = con.execute("SELECT path, hash, 'ok' AS status FROM files").fetchall()
-
-    for row in rows:
-        rel = str(row["path"])
-        if row["status"] == "parse_failed":
-            parse_failed.append(rel)
-            if rel not in modified:
-                modified.append(rel)
-        abs_path = repository / rel
-        if not abs_path.exists():
-            deleted.append(rel)
-        else:
+    # Fast path 1: Git commit diff (branch switch or commit advance)
+    git_diff_handled = False
+    if cur_commit and idx_commit and cur_commit != idx_commit:
+        diff_out = _run_git(repository, "diff", "--name-status", idx_commit, cur_commit)
+        if diff_out is not None:
+            git_diff_handled = True
+            for line in diff_out.splitlines():
+                parts = line.strip().split(maxsplit=1)
+                if len(parts) == 2:
+                    action, fpath = parts[0], parts[1]
+                    if action.startswith("D"):
+                        deleted.append(fpath)
+                    else:
+                        modified.append(fpath)
+
+    # Fast path 2: Git status when HEAD commit is unchanged
+    if not git_diff_handled and cur_commit and idx_commit and cur_commit == idx_commit:
+        status_out = _run_git(repository, "status", "--porcelain", "--untracked-files=no")
+        if status_out is not None and not status_out.strip():
+            # Working tree has zero tracked changes against HEAD
+            git_diff_handled = True
             try:
-                digest = hashlib.sha256(
-                    abs_path.read_text(encoding="utf-8", errors="replace").encode()
-                ).hexdigest()
-                if digest != row["hash"] and rel not in modified:
-                    modified.append(rel)
-            except OSError:
+                pf_rows = con.execute("SELECT path FROM files WHERE status='parse_failed'").fetchall()
+                for r in pf_rows:
+                    parse_failed.append(str(r[0]))
+                    modified.append(str(r[0]))
+            except sqlite3.OperationalError:
+                pass
+
+    if not git_diff_handled:
+        try:
+            rows = con.execute("SELECT path, hash, status, indexed_at FROM files").fetchall()
+        except sqlite3.OperationalError:
+            try:
+                rows = con.execute("SELECT path, hash, status, 0 AS indexed_at FROM files").fetchall()
+            except sqlite3.OperationalError:
+                rows = con.execute("SELECT path, hash, 'ok' AS status, 0 AS indexed_at FROM files").fetchall()
+
+        for row in rows:
+            rel = str(row["path"])
+            if row["status"] == "parse_failed":
+                parse_failed.append(rel)
                 if rel not in modified:
                     modified.append(rel)
+            abs_path = repository / rel
+            if not abs_path.exists():
+                deleted.append(rel)
+            else:
+                try:
+                    st = abs_path.stat()
+                    # Mtime check: skip reading & hashing files strictly older than indexing time
+                    idx_at = int(row["indexed_at"] or 0)
+                    if idx_at > 0 and int(st.st_mtime) < idx_at and row["status"] != "parse_failed":
+                        continue
+                    digest = hashlib.sha256(
+                        abs_path.read_text(encoding="utf-8", errors="replace").encode()
+                    ).hexdigest()
+                    if digest != row["hash"] and rel not in modified:
+                        modified.append(rel)
+                except OSError:
+                    if rel not in modified:
+                        modified.append(rel)
 
     changed = len(modified) + len(deleted)
     if changed == 0 and not parse_failed and (idx_commit == cur_commit or cur_commit is None):

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/src/codegraph/indexing/indexer.py

@@ -493,8 +493,11 @@ class Indexer:
         con = sqlite3.connect(self.db_path)
         con.row_factory = make_compat_row
         con.execute("PRAGMA journal_mode = WAL")
+        con.execute("PRAGMA synchronous = NORMAL")
         con.execute("PRAGMA foreign_keys = ON")
-        con.execute("PRAGMA busy_timeout = 5000")
+        con.execute("PRAGMA busy_timeout = 15000")
+        con.execute("PRAGMA cache_size = -64000")
+        con.execute("PRAGMA temp_store = MEMORY")
         self._ensure_schema(con)
         return con
 

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/src/codegraph/interrogation.py

@@ -1979,6 +1979,8 @@ def list_routes(
     framework: str | None = None,
     method: str | None = None,
     path: str | None = None,
+    limit: int | None = None,
+    offset: int = 0,
 ) -> dict[str, Any]:
     """Expose application routes discovered from the repository."""
     unindexed = check_index_available(con, repository)
@@ -2028,10 +2030,27 @@ def list_routes(
         for r in rows
     ]
 
+    total_count = len(routes)
+    if limit is not None:
+        safe_offset = max(0, offset)
+        safe_limit = max(0, limit)
+        paginated_routes = routes[safe_offset : safe_offset + safe_limit]
+        return {
+            "status": "ok",
+            **meta,
+            "count": len(paginated_routes),
+            "total_count": total_count,
+            "limit": safe_limit,
+            "offset": safe_offset,
+            "has_more": (safe_offset + len(paginated_routes)) < total_count,
+            "routes": paginated_routes,
+        }
+
     return {
         "status": "ok",
         **meta,
         "count": len(routes),
+        "total_count": total_count,
         "routes": routes,
     }
 

{codegraph_engine-2.1.8 → codegraph_engine-2.2.0}/src/codegraph/mcp/server.py

@@ -173,6 +173,8 @@ def create_server(
     repository: Path,
     settings: Settings | None = None,
     profile: str = "full",
+    host: str = "127.0.0.1",
+    port: int = 8765,
 ) -> Any:
     """Build an MCP FastMCP server lazily so normal CLI use needs no MCP dependency."""
     try:
@@ -184,7 +186,12 @@ def create_server(
 
     indexer = Indexer(repository, settings)
     memory = MemoryStore(indexer.db_path)
-    app = FastMCP("CodeGraph MCP", instructions=render_agent_rules("antigravity"))
+    app = FastMCP(
+        "CodeGraph MCP",
+        instructions=render_agent_rules("antigravity"),
+        host=host,
+        port=port,
+    )
     max_read_bytes = indexer.settings.max_read_bytes
 
     # -----------------------------------------------------------------------