Add smart detection to preserve .specify/ when adding agents

[DanielHashmi]

Smart Detection: Preserve User Work When Adding Agents

Problem

When users initialized a project with one agent and later wanted to add another agent, running specify init again would overwrite the .specify/ directory

Solution

Implement smart detection that automatically detects existing .specify/ directory and preserves user's work by default.

How It Works

1. Detects if .specify/ directory exists with content
2. Preserves constitution, specs, and plans automatically
3. Adds only the new agent-specific directory
4. Requires --force flag to explicitly overwrite

User Experience

specify init . --ai claude
Work on project...
specify init . --ai copilot
✅ Automatically preserves .specify/, adds .github/ directory
Shows: "Existing project detected - preserving your work"

Key Features

✅ Safe by default - Automatically preserves existing work
✅ Intuitive - Users do what feels natural (just run init again)
✅ Clear feedback - Shows what's being preserved or overwritten
✅ Explicit override - Use --force to reinitialize
✅ Backward compatible - Existing single-agent workflow unchanged

Implementation Details

Code Changes (~100 lines)

Added:

• preserve_specify parameter to download_and_extract_template() function
• Logic to skip .specify/ directory during extraction when preserve_specify=True
• Smart detection in init() function to detect existing .specify/ with content
• Clear user feedback panels for both scenarios
• Updated --force flag description

Files Modified:

• src/specify_cli/init.py (~100 lines added/modified)
• README.md (updated with examples)

Breaking Changes

None. This is a purely additive feature that improves existing behavior.

AI Assistance

This implementation was developed with assistance from Claude Code, which was utilized for both the technical implementation and the creation of this pull request description.

[Copilot]

Pull request overview

This PR implements smart detection to automatically preserve user work in the .specify/ directory when adding additional AI agents to an existing project. The key change is that running specify init in a directory with an existing .specify/ will now preserve it by default, unless the --force flag is used.

Changes:

• Added preserve_specify parameter to download_and_extract_template() function to skip .specify/ directory during extraction
• Implemented smart detection in init() function to detect existing .specify/ directories and set preservation behavior
• Updated --force flag description to reflect new behavior of forcing reinitialize/overwrite
• Added clear user feedback panels showing whether .specify/ will be preserved or overwritten
• Updated README with examples showing the new multi-agent workflow

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.

File	Description
src/specify_cli/init.py	Core implementation of smart detection and preserve_specify logic; updated function signatures and user messaging
README.md	Added documentation and examples for the new multi-agent workflow with automatic preservation

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[mnriem]

@DanielHashmi Can you address the review comments?

[DanielHashmi]

@copilot open a new pull request to apply changes based on the comments in this thread