storkit: done 370_bug_scaffold_does_not_create_mcp_json_in_project_root

.storkit/work/5_done/369_bug_cli_treats_help_and_version_as_project_paths.md

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+---
+name: "CLI treats --help and --version as project paths"
+---
+
+# Bug 369: CLI treats --help and --version as project paths
+
+## Description
+
+When running `storkit <anything>`, the binary treats the first argument as a project path, creates a directory for it, and scaffolds `.storkit/` inside. This happens for `--help`, `--version`, `serve`, `x`, or any other string. There is no validation that the argument is an existing directory or a reasonable path before creating it.
+
+## How to Reproduce
+
+1. Run `storkit --help` or `storkit serve` or `storkit x` in any directory
+2. Observe that a directory with that name is created with a full `.storkit/` scaffold inside it
+
+## Actual Result
+
+Any argument is treated as a project path and a directory is created and scaffolded. No flags are recognised.
+
+## Expected Result
+
+- `storkit --help` prints usage info and exits
+- `storkit --version` prints the version and exits
+- `storkit <path>` only works if the path already exists as a directory
+- If the path does not exist, storkit prints a clear error and exits non-zero
+
+## Acceptance Criteria
+
+- [ ] storkit --help prints usage information and exits with code 0
+- [ ] storkit --version prints the version and exits with code 0
+- [ ] storkit -h and storkit -V work as short aliases
+- [ ] storkit does not create directories for any argument — the path must already exist
+- [ ] If the path does not exist, storkit prints a clear error and exits non-zero
+- [ ] Arguments starting with - that are not recognised produce a clear error message

.storkit/work/5_done/370_bug_scaffold_does_not_create_mcp_json_in_project_root.md

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+---
+name: "Scaffold does not create .mcp.json in project root"
+---
+
+# Bug 370: Scaffold does not create .mcp.json in project root
+
+## Description
+
+Two related problems with project setup:
+
+1. When the user clicks the "project setup" button in the web UI to open a new project, the scaffold does not reliably run — the `.storkit/` directory and associated files may not be created.
+2. Even when the scaffold does run, it does not write `.mcp.json` to the project root. Without this file, agents spawned in worktrees cannot find the MCP server, causing `--permission-prompt-tool mcp__storkit__prompt_permission not found` errors and agent failures.
+
+## How to Reproduce
+
+1. Open the storkit web UI and use the project setup button to open a new project directory
+2. Check whether the full scaffold was created (`.storkit/`, `CLAUDE.md`, `script/test`, etc.)
+3. Check the project root for `.mcp.json`
+
+## Actual Result
+
+The scaffold may not run when using the UI project setup flow. When it does run, `.mcp.json` is not created in the project root. Agents fail because MCP tools are unavailable.
+
+## Expected Result
+
+Clicking the project setup button reliably runs the full scaffold, including `.mcp.json` pointing to the server's port.
+
+## Acceptance Criteria
+
+- [ ] The web UI project setup button triggers the full scaffold for new projects
+- [ ] scaffold_story_kit writes .mcp.json to the project root with the server's port
+- [ ] Existing .mcp.json is not overwritten if already present
+- [ ] .mcp.json is included in .gitignore since the port is environment-specific