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

CREATE_INDIVIDUAL_PRS.md

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+# How to Create Individual Draft PRs from Plan Branches
+
+## Current Situation
+
+All implementation plans have been created and stored in two places:
+
+1. **Organized in subdirectories** (on branch `copilot/analyze-issues-create-prs`):
+   - `plan-issue-100/PLAN.md` - npm audit vulnerabilities
+   - `plan-issue-98/PLAN.md` - glob patterns in file transfer
+   - `plan-issue-96/PLAN.md` - Windows installer fix
+   - `plan-issue-92/PLAN.md` - PM deploy.md sourcing
+   - `plan-issue-91/PLAN.md` - git worktree bug
+   - `plan-issue-90/PLAN.md` - claude --auto permissions
+   - `plan-issue-77/PLAN.md` - Slack notifications
+   - `plan-issue-76/PLAN.md` - GitHub App research
+
+2. **Individual branches** (local only, not pushed):
+   - `plan/issue-100-npm-audit`
+   - `plan/issue-98-glob-patterns`
+   - `plan/issue-96-windows-installer`
+   - `plan/issue-92-pm-deploy-md`
+   - `plan/issue-91-git-worktree`
+   - `plan/issue-90-claude-auto`
+   - `plan/issue-77-slack-notifications`
+   - `plan/issue-76-github-app-research`
+
+## Limitation
+
+The bot cannot push branches directly to the repository due to permission constraints. The `report_progress` tool only pushes to a single PR branch (`copilot/analyze-issues-create-prs`).
+
+## Manual Steps to Create Individual PRs
+
+### Option 1: Using Local Branches (Recommended)
+
+If you have push access to the repository, you can push the local branches and create PRs:
+
+```bash
+cd /path/to/apra-fleet
+
+# Push all plan branches
+for branch in plan/issue-100-npm-audit plan/issue-98-glob-patterns plan/issue-96-windows-installer plan/issue-92-pm-deploy-md plan/issue-91-git-worktree plan/issue-90-claude-auto plan/issue-77-slack-notifications plan/issue-76-github-app-research; do
+  git push origin $branch
+done
+
+# Create draft PRs using gh CLI
+gh pr create --head plan/issue-100-npm-audit --draft --title "Plan: Track and resolve npm audit vulnerabilities" --body "Implementation plan for issue #100. See PLAN.md for details."
+gh pr create --head plan/issue-98-glob-patterns --draft --title "Plan: Support glob patterns in file transfer" --body "Implementation plan for issue #98. See PLAN.md for details."
+gh pr create --head plan/issue-96-windows-installer --draft --title "Plan: Fix Windows installer file lock" --body "Implementation plan for issue #96. See PLAN.md for details."
+gh pr create --head plan/issue-92-pm-deploy-md --draft --title "Plan: Source deploy.md from git root" --body "Implementation plan for issue #92. See PLAN.md for details."
+gh pr create --head plan/issue-91-git-worktree --draft --title "Plan: Fix git worktree corruption bug" --body "Implementation plan for issue #91. See PLAN.md for details."
+gh pr create --head plan/issue-90-claude-auto --draft --title "Plan: Use claude --auto permissions" --body "Implementation plan for issue #90. See PLAN.md for details."
+gh pr create --head plan/issue-77-slack-notifications --draft --title "Plan: Slack notifications for fleet" --body "Implementation plan for issue #77. See PLAN.md for details."
+gh pr create --head plan/issue-76-github-app-research --draft --title "Research: GitHub App token limitations" --body "Research plan for issue #76. See PLAN.md for details."
+```
+
+### Option 2: Recreate from Subdirectories
+
+If the local branches are not available, you can recreate them from the subdirectories:
+
+```bash
+cd /path/to/apra-fleet
+
+# Checkout the branch with all plans
+git fetch origin
+git checkout copilot/analyze-issues-create-prs
+
+# For each issue, create a branch and copy the plan
+for issue in 100 98 96 92 91 90 77 76; do
+  git checkout -b plan/issue-${issue} origin/main
+  cp plan-issue-${issue}/PLAN.md ./PLAN.md
+  git add PLAN.md
+  git commit -m "Plan: Implementation plan for issue #${issue}"
+  git push origin plan/issue-${issue}
+done
+
+# Then create PRs as shown in Option 1
+```
+
+### Option 3: Using Git Patches
+
+Git patches have been created for each plan and can be applied:
+
+```bash
+# Patches are available in /tmp/plan-patches/ on the bot's machine
+# To use them, you would need to:
+# 1. Get the patch files from the bot
+# 2. Apply each patch to create the branch
+# 3. Push and create PRs
+
+# Example for one issue:
+git checkout -b plan/issue-100 origin/main
+git am < issue-100.patch
+git push origin plan/issue-100
+gh pr create --head plan/issue-100 --draft --title "Plan: npm audit fix" --body "Plan for #100"
+```
+
+## Automated Script
+
+A helper script is available that automates the process (requires push permissions):
+
+```bash
+#!/bin/bash
+set -e
+
+# Array of issues
+declare -A issues
+issues[100]="Track and resolve npm audit vulnerabilities"
+issues[98]="Support glob patterns and directories in file transfer"
+issues[96]="Fix Windows installer file lock issue"
+issues[92]="Source deploy.md from project git root"
+issues[91]="Fix git worktree path corruption bug"
+issues[90]="Use claude --auto permissions for Team/Enterprise"
+issues[77]="Slack notifications for fleet state changes"
+issues[76]="Research GitHub App installation token scope limitations"
+
+# For each issue
+for issue in "${!issues[@]}"; do
+  branch="plan/issue-${issue}"
+  title="${issues[$issue]}"
+
+  echo "Processing issue #${issue}..."
+
+  # Push branch
+  if git push origin ${branch} 2>/dev/null; then
+    echo "  ✓ Pushed ${branch}"
+
+    # Create PR
+    gh pr create \
+      --head ${branch} \
+      --title "Plan: ${title}" \
+      --body "Implementation plan for issue #${issue}. See PLAN.md for details." \
+      --draft && echo "  ✓ Created PR"
+  else
+    echo "  ✗ Failed to push ${branch}"
+  fi
+done
+```
+
+## Summary
+
+The bot has created all the implementation plans but cannot push them individually due to permission constraints. Manual intervention is required to:
+
+1. Push the plan branches to the repository
+2. Create individual draft PRs for each issue
+
+All necessary content is prepared and ready; it just needs to be pushed with appropriate permissions.