Shell commands in <context> sections using !` backticks trigger
permission checks for users not in dangerously-skip-permissions mode.
Replaced with @-file references where needed; process logic handles
missing files via allowed tools (Read, Glob, Grep).
Affected commands: new-project, progress, create-roadmap,
research-project, pause-work, consider-issues
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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