chore: Remove extracted code from Data Machine core

[chubes4]

Summary

After data-machine-code is working as a standalone extension, remove the duplicated code from Data Machine core. This is a separate PR on the data-machine repo.

Files to Remove Entirely

1. inc/Abilities/Fetch/GitHubAbilities.php
2. inc/Abilities/WorkspaceAbilities.php
3. inc/Core/FilesRepository/Workspace.php
4. inc/Core/FilesRepository/WorkspaceReader.php
5. inc/Core/FilesRepository/WorkspaceWriter.php
6. inc/Engine/AI/Tools/GitHubIssueTool.php
7. inc/Engine/AI/Tools/Global/GitHubTools.php
8. inc/Engine/AI/Tools/Global/WorkspaceTools.php
9. inc/Engine/AI/System/Tasks/GitHubIssueTask.php
10. inc/Cli/Commands/GitHubCommand.php
11. inc/Cli/Commands/WorkspaceCommand.php
12. inc/Core/Steps/Fetch/Handlers/GitHub/GitHub.php
13. inc/Core/Steps/Fetch/Handlers/GitHub/GitHubSettings.php

Files Requiring Surgical Edits

14. data-machine.php — Remove require_once and instantiation
15. inc/Cli/Bootstrap.php — Remove workspace and github CLI registrations
16. inc/Engine/AI/Tools/ToolServiceProvider.php — Remove WorkspaceTools
17. inc/Engine/AI/System/SystemAgentServiceProvider.php — Remove GitHubIssueTask
18. inc/Abilities/SystemAbilities.php — Remove registerGitHubIssueAbility()
19. inc/Abilities/SettingsAbilities.php — Remove github_pat/github_default_repo

Safety

• inc/Api/System/SystemContextDirective.php already has class_exists() guard — no change needed
• inc/Core/FilesRepository/DirectoryManager.php — keep get_workspace_directory() in core (shared infrastructure)

Blocked By

• data-machine-code Phase 1 completion and integration testing