- Create config.sh.example template for user configuration
- Add config-loader.sh utility for loading config with backward compatibility
- Update safety-checks.sh to use UPSTREAM_ORG and YOUR_GITHUB_USER variables
- Update list-embabel-repos.sh to use configuration variables
- Update fork-all-embabel.sh and clone-embabel-repos.sh to use config
- Update monitor-embabel.sh to use configurable repo list (MONITOR_REPOS)
- Update setup-aliases.sh to generate aliases dynamically based on config

All scripts now support configuration via config.sh while maintaining
backward compatibility with hardcoded defaults (embabel/jmjava).

Part of refactor/generify branch to make the workspace usable for any GitHub organization.

… scripts

- Update setup-upstreams.sh to use UPSTREAM_ORG and YOUR_GITHUB_USER
- Refactor sync-upstream.sh to be fully generic:
  - Removes hardcoded guide/agent repos
  - Uses MONITOR_REPOS or auto-detects from BASE_DIR
  - Uses generic upstream org and user variables
- Update my-contributions.sh to use configuration variables
- All scripts now use block_upstream_push instead of block_embabel_push

- Update check-sync-status.sh to use configuration and support generic repos
- Remove hardcoded guide/agent repos, use MONITOR_REPOS or auto-detect
- Update reset-to-upstream.sh to use UPSTREAM_ORG and YOUR_GITHUB_USER
- Both scripts now work with any repository name, not just hardcoded ones
- Update remote URLs to use generic variables

…n-commit, and prepare-commit-summaries

- Update compare-branches.sh to use MONITOR_REPOS or auto-detect repos
- Update view-pr.sh to accept any repo-name instead of hardcoded guide/agent
- Update analyze-pr-impact.sh to use generic repo-name parameter
- Update explain-commit.sh to use generic repo-name parameter
- Update prepare-commit-summaries.sh to use generic repo-name parameter

All scripts now accept any repository name from BASE_DIR and use UPSTREAM_ORG variable.

- Replace hardcoded guide/agent repos with loop over MONITOR_REPOS
- Update PR checking to iterate over all configured repos
- Update releases checking to iterate over all configured repos
- Update recent commits checking to iterate over all configured repos
- Use UPSTREAM_ORG and BASE_DIR variables

- Update get-embabel-summary.sh to use UPSTREAM_ORG and configuration
- Update list-fork-urls.sh to use YOUR_GITHUB_USER and BASE_DIR from config
- Both scripts now load configuration automatically

- Update generate-catch-up.sh to iterate over configured repos instead of hardcoded guide/agent
- Update generate-weekly-notes.sh to use MONITOR_REPOS and iterate over configured repos
- Replace hardcoded embabel/jmjava references with UPSTREAM_ORG/YOUR_GITHUB_USER variables
- Update PR checking, releases, and sync status to work with any configured repos
- Update action items generation to loop over all configured repos

- Update safe-push.sh to use block_upstream_push and check_upstream_repo (with backward compat aliases)
- Update install-git-safety-hooks.sh to use generic functions and UPSTREAM_ORG/YOUR_GITHUB_USER
- Update review-pr-workflow.sh to accept any repo-name instead of hardcoded guide/agent
- Update open-workspace.sh to generate workspace file dynamically from MONITOR_REPOS
- Update setup-git-remote.sh to use LEARNING_DIR and generic organization checks
- Update prep-for-discussion.sh and review-my-pr.sh to use configuration
- Update generate-daily-checklist.sh to load configuration (template is user-facing)

All scripts now work with any GitHub organization and user.

- Fix heredoc variable expansion issue by using echo statements instead
- Generate workspace folders dynamically from MONITOR_REPOS
- Use WORKSPACE_NAME from configuration

- Replace hardcoded 'embabel' with UPSTREAM_ORG variable
- Fix variable name from REPO to REPO_NAME

- Add configuration section at top of README.md
- Update Quick Start to include configuration setup
- Update all examples to use generic variables (UPSTREAM_ORG, YOUR_GITHUB_USER, BASE_DIR)
- Make safety section generic (works with any upstream organization)
- Update usage examples to use generic repo names
- Create comprehensive CONFIGURATION.md guide with:
  - Quick start instructions
  - All configuration variables explained
  - Multiple examples (Embabel, Spring, Apache, Custom)
  - Troubleshooting guide
  - Advanced configuration options

The workspace is now fully generic and documented for use with any GitHub organization.

- Create lightweight, self-contained test framework (test-framework.sh)
- Add unit tests for config-loader.sh (configuration loading, defaults, warnings)
- Add unit tests for safety-checks.sh (commit/push blocking, repo detection)
- Add test runner script (run-tests.sh)
- Add comprehensive test README.md with examples and documentation

Test framework features:
- No external dependencies (pure bash)
- Assertion functions (assertTrue, assertEquals, assertContains, etc.)
- Color output (green for pass, red for fail)
- Automatic test discovery
- Setup/teardown functions
- Summary reporting

Tests are working but need some refinements for result aggregation across multiple test files.

- Fix test result parsing to correctly extract counts from output
- Fix safety-checks tests to properly source functions
- Improve test file execution to prevent infinite loops
- Add verification documentation (VERIFICATION.md)
- Fix setUp/tearDown to use unique test directories per test

Tests are now verified to be running:
- 19 total tests executed
- 16 tests passing
- 3 tests failing (safety-checks functions need proper loading)

Test framework is functional and tests are executing correctly.

- Add .env-template for embabel-learning scripts with user/org settings
- Update config-loader.sh to load .env file (takes precedence over config.sh)
- Update CONFIGURATION.md to document .env usage as recommended method
- Update README.md to mention .env file as primary configuration option
- Add .env-template for guide application with Neo4j and API keys
- Add scripts/load-env.sh helper script for guide Spring Boot app
- Update guide README.md with .env configuration documentation
- Both .env and config.sh are supported (.env takes precedence)

.env files are git-ignored and contain user-specific settings.
Backward compatible with existing config.sh files.

- Update .env-template to clarify that YOUR_GITHUB_USER is personal username
- Update CONFIGURATION.md to explain UPSTREAM_ORG can be different from user org
- Add examples showing monitoring different organizations
- Clarify that UPSTREAM_ORG is the organization to monitor, not user's org
- Add real-world examples of monitoring embabel while having different username

Key point: YOUR_GITHUB_USER is your personal account (for forks),
UPSTREAM_ORG is the organization you want to monitor (can be different).

- Update testConfigLoaderWarningMessage to check for new warning message
- Update testConfigLoaderNoDuplicateWarnings to use new warning text
- Tests now check for 'No configuration file found' instead of 'config.sh not found'
- All tests now pass (19/19)

- Clarify that YOUR_GITHUB_USER is username, not org name
- Add guidance for testing vs production scenarios
- Add example for jmjava/menkelabs/embabel scenario
- Explain that personal org (menkelabs) is better for testing
- Explain that monitoring org (embabel) is for production use
- Update .env-template with testing vs production notes

Key distinction:
- YOUR_GITHUB_USER = personal username (jmjava)
- Personal org (menkelabs) = good for testing
- UPSTREAM_ORG (embabel) = organization to monitor in production

- Add TEST_UPSTREAM_ORG parameter to .env-template for test organization
- Update config-loader.sh to use TEST_UPSTREAM_ORG when TEST_MODE=true
- Update run-tests.sh to set TEST_MODE=true before loading config
- Update CONFIGURATION.md to document TEST_UPSTREAM_ORG feature

Benefits:
- No manual switching between test and production orgs
- Production scripts always use UPSTREAM_ORG (e.g., embabel)
- Test scripts automatically use TEST_UPSTREAM_ORG (e.g., menkelabs)
- Clear separation of test vs production configurations
- Safer testing with personal orgs

Usage:
  UPSTREAM_ORG=embabel         # Production
  TEST_UPSTREAM_ORG=menkelabs  # Testing (optional)

- Add block-upstream-commit as local pre-commit hook
- Hook runs safety checks (block_upstream_commit) on every commit
- Loads config-loader.sh to get UPSTREAM_ORG from .env
- Safety checks now run automatically alongside ggshield
- All commits from scripts will run both ggshield and safety checks

This ensures:
- Secret scanning (ggshield) runs on every commit
- Safety checks prevent commits to upstream org repos
- Both hooks run automatically, no manual intervention needed

- Run pre-commit migrate-config to fix deprecated stage names
- Configuration now uses current pre-commit standards
- All hooks still working correctly

- Update 'What's Included' section to list safety checks
- Document that safety checks use UPSTREAM_ORG from .env
- Update 'How It Works' section to mention pre-commit hooks
- Add safety checks to 'What Gets Checked' table
- Clarify that all commits automatically run both ggshield and safety checks
- Document that hooks run automatically on every commit

Key points:
- GitGuardian (ggshield) runs on every commit
- Safety checks (block-upstream-commit) run on every commit
- Both hooks are integrated into pre-commit framework
- Uses UPSTREAM_ORG from .env configuration
- All hooks run automatically, no manual intervention needed

- Configure ggshield to run on pre-push stage (in addition to pre-commit)
- Add block-upstream-push hook for pre-push stage
- Create block-upstream-push-hook.sh wrapper script for pre-push hooks
- Update README to document that git push invokes hooks automatically
- Update 'What Gets Checked' table to show push hooks
- Fix detect-secrets false positive in commit summary file

Answer to user question:
✅ YES - git push will work in embabel-learning repo
✅ YES - git push WILL invoke GitGuardian (ggshield) hooks automatically
✅ YES - git push WILL invoke safety checks (block-upstream-push) automatically

When you run git push:
  1. ggshield (GitGuardian) runs automatically
  2. block-upstream-push (safety checks) runs automatically
  3. All other pre-push hooks run automatically

This ensures:
- Secret scanning on every push (ggshield)
- Safety checks prevent pushes to upstream org repos
- All hooks run automatically, no manual steps needed