Fix/medium priority issues

[stefankudev]

Summary

Fix 10 high/medium priority issues for v1.0 readiness and merge 4 dependabot dependency updates.

Related Issues

• Closes High no.3: Error Handling Divergence
• Closes High no.4: Dangerous Panic Hook Re-wrapping
• Closes High no.5: Status Messages Cleared Immediately
• Closes Medium no.6: Integer Overflow in Size Calculation
• Closes Medium no.7: Hardcoded SKIP_DIRS Not Configurable
• Closes Medium no.8: Background Thread Termination Is Silent
• Closes Medium no.9: Unused Parameter in Render Function
• Closes Medium no.12: No Validation of Ecosystem Configuration Files
• Closes Medium no.14: No Recovery From Partial Deletion
• Closes Medium no.15: Wrong Default for Confidence Enum
• Closes Medium no.16: Unclear Default Ecosystem Behavior
• Supersedes dependabot PR chore(deps): update crossterm requirement from 0.27 to 0.29 #12 (crossterm 0.27→0.29)
• Supersedes dependabot PR chore(deps): update dirs requirement from 5.0 to 6.0 #11 (dirs 5.0→6.0)
• Supersedes dependabot PR chore(deps): update ratatui requirement from 0.29 to 0.30 #10 (ratatui 0.29→0.30)
• Supersedes dependabot PR for actions/checkout v4→v6

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Refactoring

Changes

Error Handling & Safety

• run() and run_plain() now return Result<()> with proper error propagation via anyhow::Context
• main.rs handles errors gracefully instead of panicking
• Added atomic flag to prevent panic hook double-wrapping
• Status messages now persist for 5 seconds before auto-clearing

Scanner

• Size calculation uses saturating_add() to prevent integer overflow
• SKIP_DIRS (.git, .svn, .hg, etc.) merged with --exclude flag to allow user override

UI

• Removed unused _viewport_height parameter from render() function
• Added debug logging when background scan thread terminates

Config

• Returns error if no valid ecosystem JSON files are found during loading
• Changed Confidence enum default from Certain to Undetected

Deleter

• Replaced std::fs::remove_dir_all() with trash::delete() for safe deletion with recovery support

Dependencies

• crossterm: 0.27 → 0.29
• dirs: 5.0 → 6.0
• ratatui: 0.29 → 0.30
• actions/checkout: v4 → v6

Checklist

• My code follows the style guidelines of this project.
• I have performed a self-review of my own code.
• I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• I have added tests that prove my fix is effective or that my feature works.
• New and existing unit tests pass locally with my changes.