chore: remove closed issue documentation files

Removed 28 closed issue documentation files from docs/issues/:
- #16: epic-finish-configure-command-system-security (epic)
- #19: refactor-ansible-templates-variables-pattern
- #102: epic-user-output-architecture-improvements (epic)
- #103: extract-verbosity-filtering-logic
- #105: create-variables-template
- #106: convert-firewall-template-to-static
- #112: epic-refactor-and-improve-e2e-test-execution (epic)
- #113: 1-1-create-dependency-installation-package-for-e2e-tests
- #114: 1-1-1-create-detection-logic-package
- #115: 1-1-2-create-cli-binary-with-check-command
- #116: 1-1-3-create-docker-test-infrastructure
- #117: 1-1-4-implement-installation-logic
- #118: 1-2-integrate-dependency-installer-with-e2e-tests
- #119: 1-3-update-ci-workflows-and-remove-bash-scripts
- #120: 1-4-configure-github-copilot-agent-environment
- #121: 1-5-install-git-precommit-hooks-for-copilot
- #123: simplify-test-infrastructure
- #124: add-theme-configuration-support
- #127: use-message-trait-for-extensibility
- #128: parameterized-test-cases
- #133: add-formatter-override-support
- #135: type-safe-channel-routing-for-user-output
- #138: add-buffering-control
- #139: builder-pattern-for-complex-messages
- #140: output-sink-abstraction
- #146: 1-6-update-precommit-script-for-github-runner-compatible-e2e-tests
- #147: 1-7-configure-copilot-agent-firewall-for-dependency-installer
- #149: refactor-user-output-module-to-folder-structure

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

Remaining open issues: #96, #154, #155, #156

Author: josecelano