feat: Add Logseq TODO generator to IssueManager

[theinterneti]

This PR adds a new command logseq-todo to scripts/issue_manager.py that generates Logseq-formatted TODO blocks from GitHub issues. This facilitates the workflow defined in .github/instructions/logseq-knowledge-base.instructions.md.

Features:

• Generates TODOs with correct tags, priority, and type based on issue labels.
• Includes links to the issue and assignee information.
• Adds unit tests in tests/test_issue_manager_logseq.py.

This PR replaces the feature part of #125, which was polluted with infrastructure changes.

[github-actions]

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[Copilot]

Pull request overview

This PR adds a new logseq-todo command to scripts/issue_manager.py that generates Logseq-formatted TODO blocks from GitHub issues. This feature supports the workflow documented in .github/instructions/logseq-knowledge-base.instructions.md by automating the creation of properly formatted TODOs with tags, priorities, types, and metadata based on GitHub issue labels.

Key Changes:

• Added logseq-todo command to issue manager for generating Logseq-formatted TODOs from GitHub issues
• Added comprehensive unit tests for the new functionality
• Updated documentation and configuration files to reflect repository reorganization

Reviewed changes

Copilot reviewed 15 out of 1176 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
_archive/nested_copies/TTA.dev	Added subproject commit reference
_archive/README.md	Removed archive directory documentation (file deleted)
README.md	Updated repository structure to include additional directories (config, docs, playbooks, scripts, tests)
PRIMITIVES_CATALOG.md	Added documentation for GitCollaborationPrimitive and collaboration primitives category
CONTRIBUTING.md	Updated type checking paths from packages/ to platform/ apps/
.vscode/settings.json	Updated Python interpreter path to absolute path
.serena/project.yml	Added Serena project configuration file
.serena/.gitignore	Added gitignore for Serena cache directory
.hypertool/mcp_servers.json	Extensive updates to MCP server configurations including new servers and environment variable changes
.github/copilot-instructions.md	Updated test coverage paths from packages to platform and apps
.agent-notifications/*.json	Added multiple agent notification files for tracking commits

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[Copilot]

Hard-coded absolute path to user's home directory should be replaced with a relative path or environment variable. Use .venv/bin/python instead to ensure portability across different development environments.

Suggested change

	"python.defaultInterpreterPath": "/home/thein/repos/TTA.dev-copilot/.venv/bin/python",
	"python.defaultInterpreterPath": ".venv/bin/python",

[Copilot]

Hard-coded absolute path to user's home directory should be replaced with a relative path or environment variable to ensure portability across different development environments.

Suggested change

	"--project", "/home/thein/repos/TTA.dev-cline"
	"--project", "${HOME}/repos/TTA.dev-cline"

[Copilot]

Agent notification files contain hard-coded absolute paths that may not be portable across environments. Consider if these files should be tracked in version control, as they appear to be runtime/instance-specific data.

Suggested change

"worktree": "/home/thein/repos/TTA.dev",

[Copilot]

Agent notification files contain hard-coded absolute paths that may not be portable across environments. Consider if these files should be tracked in version control, as they appear to be runtime/instance-specific data.

[Copilot]

Agent notification files contain hard-coded absolute paths that may not be portable across environments. Consider if these files should be tracked in version control, as they appear to be runtime/instance-specific data.

Suggested change

"worktree": "/home/thein/repos/TTA.dev-cline",

[Copilot]

Agent notification files contain hard-coded absolute paths that may not be portable across environments. Consider if these files should be tracked in version control, as they appear to be runtime/instance-specific data.

[Copilot]

Agent notification files contain hard-coded absolute paths that may not be portable across environments. Consider if these files should be tracked in version control, as they appear to be runtime/instance-specific data.

Suggested change

"worktree": "/home/thein/repos/TTA.dev-cline",

The best way to fix the problem is to parse the input URL first, and then check the hostname (and optionally scheme) to see if it matches gitmcp.io or a subdomain thereof. Specifically, use urlparse to extract the hostname and match it with either 'gitmcp.io' or strings that end with .gitmcp.io. This ensures the logic only triggers on true gitmcp.io domains and is not confused by other parts of the URL containing the substring. The edit should be made in the parse_repo_uri method in scripts/mcp/config_parser.py, specifically replacing the substring check on line 55 with a check on the parsed hostname.

---

The best way to fix the problem is, rather than checking for "github.com" as a substring in the URL, to parse the URL using urlparse and then verify that its hostname is exactly "github.com" or ends with .github.com (if you want to allow subdomains). The change should occur within the method parse_repo_uri, specifically on line 66 where the check is performed. No changes to the rest of the code are necessary; just update the logic for checking the GitHub hostname.

All necessary imports (from urllib.parse import urlparse) are already present.

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The best way to fix this is to parse repo_uri as a URL with urlparse and check that its host matches gitmcp.io, rather than simply checking if the string "gitmcp.io" is present anywhere in repo_uri. This also applies to the next check for "github.com". Both cases should guard against subdomain spoofing. The safest fix is to parse the host, then check that it is exactly (or ends with .gitmcp.io/.github.com if subdomains are allowed) the target domain. The string method used here is for generating a default name, so the logic should stay unchanged except for the host matching, preserving function.

Edits should be made in the method add_repo_uri() between lines 223 and 234, affecting the conditional chains using substring checks for gitmcp.io and github.com. The code should use urlparse to extract the host (hostname). If using a non-standard URL scheme (i.e., npm: or docker:), the string-based logic can remain unchanged for those cases. Only the checks for git-hosted URLs using HTTP/HTTPS should use host-based parsing.

No additional imports are necessary, as urlparse is already imported.

To fix this bug, the code should parse the repository URI and check if its hostname matches github.com instead of checking if "github.com" appears anywhere in the string. Use Python's urlparse from the standard library to parse the URI, then check parsed_url.hostname. Update line 226 (and the surrounding relevant logic) to use this safer check. This change will ensure that only URLs whose host is github.com are classified as such (when generating a default name). No new functionality is introduced, only safer behavior.