Add cleanup script and replace chmod patterns with bash invocation

[Copilot]

• Create cleanup.sh - fully commented-out bash script for deleting leftover files
• Add "Protocol: Cleanup Leftover Files" section in AGENTS.md
• Replace chmod +x / ./script.sh patterns with bash script.sh across all files
• Add warning about empty EXPECTED_FILES in AGENTS.md (review comment)
• Document git restore cleanup.sh for re-commenting (review comment)
• Fix ./cleanup.sh → bash cleanup.sh in script USAGE header (review comment)
• Use -path './.git' -prune for empty dir cleanup (review comment)
• Use git rev-parse for repo-root detection instead of [ ! -d ".git" ] (review comment)
• Add guard that aborts when EXPECTED_FILES is empty/unset (review comment)
• Use git ls-files instead of bare find for file discovery (review comment)
• Use rm -- instead of rm to handle paths starting with - (review comment)
• Run code review and security checks

Original prompt

include a bash script that is fully commented out that is soul purpouse is the delete the files that are leftover when new codebase is created and dosnt match the original repos file structure. add this as a protocol in AGENTS.md when prompted and only when the llm is prompted

Custom agent used: documentation-builder
Specialized agent for building README.md and AGENTS.md files from template versions

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[Copilot]

Pull request overview

Adds an on-demand, inert-by-default cleanup mechanism to remove scaffolding leftovers that diverge from the canonical template repo structure, plus a documented protocol for invoking it intentionally.

Changes:

• Introduces cleanup.sh as a fully commented-out cleanup script intended for manual/LLM-prompted use only.
• Documents an explicit “Protocol: Cleanup Leftover Files” workflow in AGENTS.md, including steps, checklist, and agent invocation examples.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 8 comments.

File	Description
cleanup.sh	Adds an inert cleanup script that can diff current files vs an expected list and delete leftovers after confirmation.
AGENTS.md	Adds a protocol section describing how/when to run the cleanup script and how to safely execute the workflow.

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[swarm-protocol]

@copilot apply changes based on the comments in this thread

[Copilot]

@copilot apply changes based on the comments in this thread

Applied all 8 review comments in commit a5b99f6. The 4 that were already addressed (AGENTS.md warning, git restore docs, bash cleanup.sh usage, .git prune) were verified in place. The 4 remaining changes applied to cleanup.sh:

1. Repo-root detection now uses git rev-parse --show-toplevel instead of [ ! -d ".git" ]
2. Added a guard that aborts with an error if EXPECTED_FILES is empty/unset
3. File discovery now uses git ls-files + git ls-files --others --exclude-standard instead of bare find
4. Changed rm "$file" to rm -- "$file" for paths starting with -