story-kit: done 347_story_mcp_tool_for_shell_command_execution

.story_kit/work/1_backlog/341_story_rename_story_kit_directory_to_storkit.md

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-name: "Rename .story_kit directory to .storkit"
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-
-# Story 341: Rename .story_kit directory to .storkit
-
-## User Story
-
-As a project owner, I want the config directory renamed from .story_kit to .storkit, so that the directory name matches the new binary and product name.
-
-## Acceptance Criteria
-
-- [ ] Rename the physical directory from .story_kit to .storkit
-- [ ] All server code references to .story_kit paths updated to .storkit
-- [ ] All .gitignore references updated
-- [ ] bot.toml and project.toml paths updated
-- [ ] CLAUDE.md references updated
-- [ ] Watcher, worktree, and pipeline code updated
-- [ ] MCP tool descriptions updated if they reference .story_kit
-- [ ] Agent prompts updated if they reference .story_kit
-- [ ] No backwards compatibility — .story_kit simply stops working, users must rename to .storkit
-
-## Out of Scope
-
-- TBD

.story_kit/work/1_backlog/346_story_mcp_tools_for_file_operations_read_write_edit_list.md

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-name: "MCP tools for file operations (read, write, edit, list)"
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-
-# Story 346: MCP tools for file operations (read, write, edit, list)
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-## User Story
-
-As a non-Claude agent connected via MCP, I want file operation tools so that I can read, write, and edit code in my worktree.
-
-## Acceptance Criteria
-
-- [ ] read_file tool — reads file contents, supports offset/limit for large files
-- [ ] write_file tool — writes/creates a file at a given path
-- [ ] edit_file tool — replaces a string in a file (old_string/new_string like Claude Code's Edit)
-- [ ] list_files tool — glob pattern matching to find files in the worktree
-- [ ] All operations scoped to the agent's worktree path for safety
-- [ ] Returns clear errors for missing files, permission issues, etc.
-
-## Out of Scope
-
-- TBD

.story_kit/work/1_backlog/347_story_mcp_tool_for_shell_command_execution.md

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-name: "MCP tool for shell command execution"
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-
-# Story 347: MCP tool for shell command execution
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-## User Story
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-As a non-Claude agent connected via MCP, I want a shell command tool so that I can run cargo build, npm test, and other commands in my worktree.
-
-## Acceptance Criteria
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-- [ ] run_command tool — executes a bash command and returns stdout/stderr/exit_code
-- [ ] Command runs in the agent's worktree directory
-- [ ] Supports timeout parameter (default 120s, max 600s)
-- [ ] Sandboxed to worktree — cannot cd outside or access host paths
-- [ ] Returns streaming output for long-running commands
-- [ ] Dangerous commands blocked (rm -rf /, etc.)
-
-## Out of Scope
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-- TBD