storkit: create 370_bug_scaffold_does_not_create_mcp_json_in_project_root

.storkit/work/1_backlog/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
+
+When storkit scaffolds a new project, 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. Create a new empty directory and run `storkit /path/to/new-project`
+2. Check the project root for `.mcp.json`
+
+## Actual Result
+
+`.mcp.json` is not created in the project root. Only worktrees get `.mcp.json` written (via `write_mcp_json` in `worktree.rs`). Agents fail because MCP tools are unavailable.
+
+## Expected Result
+
+The scaffold writes `.mcp.json` to the project root pointing to the server's port, so agents and the CLI can discover the MCP endpoint.
+
+## Acceptance Criteria
+
+- [ ] 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