chore: remove closed issue documentation files

Removed 7 closed issue documentation files from docs/issues/:
- #56: Refactor Command Handlers to Modular Directory Structure
- #58: Refactor Presentation Commands to Modular Directory Structure
- #85: Coverage & Reporting EPIC
- #86: Add coverage check to pre-commit script
- #87: Create coverage CI workflow
- #88: Refactor testing documentation structure
- #89: Write coverage documentation

All these issues have been closed on GitHub and no longer need
local documentation files.

Remaining open issues: #16, #17, #18, #19, #79, #80, #96

Author: josecelano