Adds ability to specify custom spec directory via --spec-dir parameter in specify init command. Updates CLI help documentation, refactors bash and PowerShell scripts to support custom directories via SPECIFY_SPEC_DIR environment variable, updates templates to use {SPEC_DIR} placeholder instead of hardcoded "specs", and adds validation for custom directory paths. Maintains backward compatibility by defaulting to "specs" directory.

Introduce pytest-based testing framework with dependencies and comprehensive validation suite for the new --spec-dir capability:- Add pytest and pytest-cov to project dependencies in pyproject.toml- Create test fixtures and configuration in conftest.py for consistent test setup- Implement 1100+ lines of test coverage across 5 specialized test modules- Cover edge cases including path traversal prevention, character validation, and unicode handling- Test both CLI integration and unit-level function validation- Verify file reference updates and directory renaming behaviorThe test infrastructure ensures reliability of the spec directory customization feature through thorough validation of input constraints, error handling, and functional correctness across multiple scenarios.

…ges and edge case handlingEnhance the spec directory validation system to provide better user experience and handle edge cases more robustly:- Improved validation with detailed error messages and helpful tips- Added support for Unicode characters in directory names- Enhanced parent traversal and absolute path detection- Added reserved Windows system name validation- Better control character and invalid character detection- More precise regex patterns in update_spec_directory_references function- Consolidated test coverage in test_validate_spec_dir.py with comprehensive scenarios- Removed redundant test file test_spec_dir_validation.py- Minor improvements to helper function sourcing in bash/powershell scriptsThese changes make validation more comprehensive while maintaining backward compatibility and providing clearer feedback to users when validation fails.

…anch- Merge new AI agents (shai, bob) with --spec-dir option support- Keep both rate limiting functions and spec directory validation- Preserve remote branch checking logic while maintaining clean code structure- Use {SPEC_DIR} variable in templates for custom spec directory support- Update documentation to include both new featuresAll functionality preserved:- --spec-dir option works for custom specification directories- New AI agents (shai, bob) are available- Enhanced error handling with rate limiting- Improved remote branch detection- Scripts support both custom spec dirs and new agents

Allow SPECIFY_SPEC_DIR environment variable to override default specs directory,providing more flexibility in configuration management.

Updated the spec_dir option to properly handle empty environment variablesby checking if the value exists and is not blank before using it,otherwise falling back to the default 'specs' directory.

…le functionalityAdds a new test file with extensive test coverage for the SPECIFY_SPEC_DIRenvironment variable, including validation of different path formats,fallback behavior when unset or empty, and precedence over command line flags.Also updates existing integration test to verify correct default spec dir usage.

…ssues- Fix MD060 table column style errors in docs/index.md, docs/upgrade.md, and docs/local-development.md  by converting tables to compact style with proper pipe spacing- Fix MD060 alignment errors in README.md, templates/analyze.md, and templates/plan-template.md  by adjusting table separator lines for compact style compliance- Fix MD005 list indentation error in templates/commands/specify.md- Fix MD029 ordered list prefix errors in templates/commands/clarify.md- Fix MD046 code block style false positive in templates/commands/clarify.mdTotal: 25 markdownlint errors resolved → 0 errors