#105 Fix: Only remove agent context files if not tracked by git

[Anonymous]

Originally created by: Copilot

• [x] Create implementation plans for 8 complex issues (#76, [#77], [#90], [#91], [#92], [#96], [#98], [#100])
• [x] Organize plans in subdirectories (plan-issue-N/PLAN.md)
• [x] Create local branches for each plan (plan/issue-N)
• [x] Create git patches as backup
• [x] Document manual steps (CREATE_INDIVIDUAL_PRS.md)
• [x] Create task completion summary (SUMMARY.md)
• [ ] Manual step: Push plan branches and create individual draft PRs (requires push permissions)

[Anonymous]

• assigned_to: Copilot

[Anonymous]

• assigned_to: kumaakh