feat: bundle comments and file ignore

docs/cli-reference.mdx

@@ -251,6 +251,7 @@ mcp-agent deploy <APP_NAME> [OPTIONS]
 | `--dry-run` | Validate without deploying | `false` |
 | `--api-url` | API base URL | `https://deployments.mcp-agent.com` |
 | `--api-key` | API key | From env or config |
+| `--ignore-file <path>` | Use a specific ignore file (gitignore syntax). Defaults to `.mcpacignore` if present. | None |
 
 **Examples:**
 ```bash
@@ -264,8 +265,16 @@ mcp-agent deploy my-agent \
 
 # Dry run
 mcp-agent deploy my-agent --dry-run
+
+# Use a custom ignore file
+mcp-agent deploy my-agent --ignore-file .deployignore
 ```
 
+Ignore file usage
+
+- Detection order: 1) `--ignore-file <path>` (highest precedence), 2) `.mcpacignore` in `--config-dir`, 3) `.mcpacignore` in the working directory (CWD).
+- Patterns follow gitignore syntax and are evaluated relative to `--config-dir`.
+
 ### mcp-agent cloud configure
 
 Configure access to a deployed MCP app.
@@ -489,4 +498,4 @@ mcp-agent deploy my-agent --dry-run
 - [Configuration Guide](/configuration)
 - [Cloud Deployment](/cloud/getting-started)
 - [Workflow Patterns](/workflows/overview)
-- [Examples](https://github.com/lastmile-ai/mcp-agent/tree/main/examples)
+- [Examples](https://github.com/lastmile-ai/mcp-agent/tree/main/examples)

docs/cloud/overview.mdx

@@ -24,6 +24,8 @@ description: "[In beta] Deploy and manage AI agents as MCP servers"
 
 <Note>When packaging your mcp-agent app for the cloud, our CLI will be searching for `main.py`. The entire directory will be deployed, so you can reference other files and upload other assets.</Note>
 
+<Note>You can optionally exclude files from the bundle using an ignore file (gitignore syntax). Precedence: 1) `--ignore-file <path>` (explicit override), 2) `.mcpacignore` in `--config-dir`, 3) `.mcpacignore` in the working directory (CWD).</Note>
+
 2. Make sure you have either a `pyproject.toml` or a `requirements.txt` file in your app directory.
 
 3. Mark your functions that you'd like to be tool calls with the `@app.tool` decorators

pyproject.toml

@@ -76,6 +76,7 @@ crewai = [
 cli = [
     "hvac>=1.1.1",
     "httpx>=0.28.1",
+    "pathspec>=0.12.1",
     "pyjwt>=2.10.1",
     "typer[all]>=0.15.3",
     "watchdog>=6.0.0"

src/mcp_agent/cli/cloud/commands/deploy/bundle_utils.py

@@ -0,0 +1,80 @@
+"""Ignore-file helpers for the deploy bundler.
+
+This module focuses on two things:
+- Parse an ignore file (gitignore-compatible syntax) into a `PathSpec` matcher.
+- Provide an adapter that works with `shutil.copytree(ignore=...)` to decide
+  which directory entries to skip during a copy.
+
+There is no implicit reading of `.gitignore` here. Callers must explicitly
+pass the ignore file path they want to use (e.g., `.mcpacignore`).
+"""
+
+from pathlib import Path
+from typing import Optional, Set
+import pathspec
+
+
+def create_pathspec_from_gitignore(ignore_file_path: Path) -> Optional[pathspec.PathSpec]:
+    """Create and return a `PathSpec` from an ignore file.
+
+    The file is parsed using the `gitwildmatch` (gitignore) syntax. If the file
+    does not exist, `None` is returned so callers can fall back to default
+    behavior.
+
+    Args:
+        ignore_file_path: Path to the ignore file (e.g., `.mcpacignore`).
+
+    Returns:
+        A `PathSpec` that can match file/directory paths, or `None`.
+    """
+    if not ignore_file_path.exists():
+        return None
+
+    with open(ignore_file_path, "r", encoding="utf-8") as f:
+        spec = pathspec.PathSpec.from_lines("gitwildmatch", f)
+
+    return spec
+
+
+
+def should_ignore_by_gitignore(
+    path_str: str, names: list, project_dir: Path, spec: Optional[pathspec.PathSpec]
+) -> Set[str]:
+    """Return the subset of `names` to ignore for `shutil.copytree`.
+
+    This function is designed to be passed as the `ignore` callback to
+    `shutil.copytree`. For each entry in the current directory (`path_str`), it
+    computes the path relative to the `project_dir` root and checks it against
+    the provided `spec` (a `PathSpec` created from an ignore file).
+
+    Notes:
+    - If `spec` is `None`, this returns an empty set (no additional ignores).
+    - For directories, we also check the relative path with a trailing slash
+      (a common gitignore convention).
+    """
+    if spec is None:
+        return set()
+
+    ignored: Set[str] = set()
+    current_path = Path(path_str)
+
+    for name in names:
+        full_path = current_path / name
+        try:
+            rel_path = full_path.relative_to(project_dir)
+        except ValueError:
+            # If `full_path` is not under `project_dir`, ignore matching is skipped.
+            continue
+
+        # Normalize to POSIX separators so patterns work cross-platform (Windows too)
+        rel_path_str = rel_path.as_posix()
+
+        # Match files exactly; for directories also try with a trailing slash
+        # to respect patterns like `build/`.
+        if spec.match_file(rel_path_str):
+            ignored.add(name)
+        elif full_path.is_dir() and spec.match_file(rel_path_str + "/"):
+            ignored.add(name)
+
+
+    return ignored

src/mcp_agent/cli/cloud/commands/deploy/main.py

@@ -116,6 +116,19 @@ def deploy_config(
         min=1,
         max=10,
     ),
+    ignore_file: Optional[Path] = typer.Option(
+        None,
+        "--ignore-file",
+        help=(
+            "Path to ignore file (gitignore syntax). Precedence: 1) --ignore-file <path>, "
+            "2) .mcpacignore in --config-dir, 3) .mcpacignore in working directory."
+        ),
+        exists=False,
+        readable=True,
+        dir_okay=False,
+        file_okay=True,
+        resolve_path=True,
+    ),
 ) -> str:
     """Deploy an MCP agent using the specified configuration.
 
@@ -324,13 +337,24 @@ def deploy_config(
             else:
                 print_info("Skipping git tag (not a git repository)")
 
+        # Determine effective ignore path
+        ignore_path: Optional[Path] = None
+        if ignore_file is not None:
+            ignore_path = ignore_file
+        else:
+            candidate = config_dir / ".mcpacignore"
+            if not candidate.exists():
+                candidate = Path.cwd() / ".mcpacignore"
+            ignore_path = candidate if candidate.exists() else None
+
         app = run_async(
             _deploy_with_retry(
                 app_id=app_id,
                 api_key=effective_api_key,
                 project_dir=config_dir,
                 mcp_app_client=mcp_app_client,
                 retry_count=retry_count,
+                ignore=ignore_path,
             )
         )
 
@@ -359,6 +383,7 @@ async def _deploy_with_retry(
     project_dir: Path,
     mcp_app_client: MCPAppClient,
     retry_count: int,
+    ignore: Optional[Path],
 ):
     """Execute the deployment operations with retry logic.
 
@@ -378,6 +403,7 @@ async def _deploy_with_retry(
             app_id=app_id,
             api_key=api_key,
             project_dir=project_dir,
+            ignore_file=ignore,
         )
     except Exception as e:
         raise CLIError(f"Bundling failed: {str(e)}") from e

src/mcp_agent/cli/cloud/commands/deploy/wrangler_wrapper.py

@@ -18,6 +18,10 @@
     utc_iso_now,
 )
 
+from .bundle_utils import (
+    create_pathspec_from_gitignore,
+    should_ignore_by_gitignore,
+)
 from .constants import (
     CLOUDFLARE_ACCOUNT_ID,
     CLOUDFLARE_EMAIL,
@@ -107,7 +111,9 @@ def _handle_wrangler_error(e: subprocess.CalledProcessError) -> None:
         print_error(clean_output)
 
 
-def wrangler_deploy(app_id: str, api_key: str, project_dir: Path) -> None:
+def wrangler_deploy(
+    app_id: str, api_key: str, project_dir: Path, ignore_file: Path | None = None
+) -> None:
     """Bundle the MCP Agent using Wrangler.
 
     A thin wrapper around the Wrangler CLI to bundle the MCP Agent application code
@@ -128,6 +134,7 @@ def wrangler_deploy(app_id: str, api_key: str, project_dir: Path) -> None:
         app_id (str): The application ID.
         api_key (str): User MCP Agent Cloud API key.
         project_dir (Path): The directory of the project to deploy.
+        ignore_file (Path | None): Optional path to a gitignore-style file for excluding files from the bundle.
     """
 
     # Copy existing env to avoid overwriting
@@ -165,18 +172,41 @@ def wrangler_deploy(app_id: str, api_key: str, project_dir: Path) -> None:
     with tempfile.TemporaryDirectory(prefix="mcp-deploy-") as temp_dir_str:
         temp_project_dir = Path(temp_dir_str) / "project"
 
-        # Copy the entire project to temp directory, excluding unwanted directories and secrets file
-        def ignore_patterns(_path, names):
+        # Load ignore rules (gitignore syntax) only if an explicit ignore file is provided
+        ignore_spec = (
+            create_pathspec_from_gitignore(ignore_file) if ignore_file else None
+        )
+        if ignore_file:
+            if ignore_spec is None:
+                print_warning(
+                    f"Ignore file '{ignore_file}' not found; applying default excludes only"
+                )
+            else:
+                print_info(f"Using ignore patterns from {ignore_file}")
+        else:
+            print_info("No ignore file provided; applying default excludes only")
+
+        # Copy the entire project to temp directory, excluding unwanted directories and the live secrets file
+        def ignore_patterns(path_str, names):
             ignored = set()
+
+            # Keep existing hardcoded exclusions (highest priority)
             for name in names:
                 if (name.startswith(".") and name not in {".env"}) or name in {
                     "logs",
                     "__pycache__",
                     "node_modules",
                     "venv",
-                    MCP_SECRETS_FILENAME,
+                    MCP_SECRETS_FILENAME,  # Exclude mcp_agent.secrets.yaml only
                 }:
                     ignored.add(name)
+
+            # Apply explicit ignore file patterns (if provided)
+            spec_ignored = should_ignore_by_gitignore(
+                path_str, names, project_dir, ignore_spec
+            )
+            ignored.update(spec_ignored)
+
             return ignored
 
         shutil.copytree(project_dir, temp_project_dir, ignore=ignore_patterns)
@@ -209,6 +239,26 @@ def ignore_patterns(_path, names):
                 # Rename in place
                 file_path.rename(py_path)
 
+        # Compute and log which original files are being bundled (skip internal helpers)
+        bundled_original_files: list[str] = []
+        internal_bundle_files = {"wrangler.toml", "mcp_deploy_breadcrumb.py"}
+        for root, _dirs, files in os.walk(temp_project_dir):
+            for filename in files:
+                rel = Path(root).relative_to(temp_project_dir) / filename
+                if filename in internal_bundle_files:
+                    continue
+                if filename.endswith(".mcpac.py"):
+                    orig_rel = str(rel)[: -len(".mcpac.py")]
+                    bundled_original_files.append(orig_rel)
+                else:
+                    bundled_original_files.append(str(rel))
+
+        bundled_original_files.sort()
+        if bundled_original_files:
+            print_info(f"Bundling {len(bundled_original_files)} project file(s):")
+            for p in bundled_original_files:
+                console.print(f" - {p}")
+
         # Collect deployment metadata (git if available, else workspace hash)
         git_meta = get_git_metadata(project_dir)
         deploy_source = "git" if git_meta else "workspace"