fix: private repository support and parser compatibility

[anschmieg]

Summary

Fixes issues with adding and viewing private repositories.

Changes

URL Parsing Fix

• Handle trailing slashes in repo URLs (e.g., https://github.com/user/repo/)
• Previously caused 'Repository not found' errors

Private Repo Authentication

• Add onAuth to git.pull() - was missing authentication for private repos
• Clone worked but pull failed silently, causing the request to hang

Parser ESM/CJS Fix

• Replace unified().use(remarkParse) with remark().parse()
• unified v11+ has ESM/CJS compatibility issues with require()
• Fixes 'Cannot parse without Parser' errors

Testing

1. Add a private repository URL (with or without trailing slash)
2. Click on the repo to list .qmd files
3. Open a .qmd file - should render without errors

[Copilot]

Pull request overview

This pull request fixes critical issues with private repository support and improves parser compatibility for the Quartorium application. The changes address three main problems: URL parsing failures with trailing slashes, missing authentication for git pull operations on private repos, and ESM/CJS compatibility issues with the unified/remark parser.

• Fixed URL parsing to handle trailing slashes in repository URLs
• Added authentication (onAuth) to git.pull() for private repository access
• Migrated from unified().use(remarkParse) to remark().parse() to resolve ESM/CJS compatibility issues

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
backend/src/core/quartoParser.js	Simplifies markdown parsing by switching to remark's built-in parser, fixing ESM/CJS compatibility issues
backend/src/api/repos.routes.js	Adds trailing slash handling in URL parsing, authentication for git pull operations, and improves error logging for debugging

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

The order of operations in the URL cleanup could leave a trailing slash in edge cases. For example, a URL ending in /.git would result in user/repo/ after .git is removed. Consider swapping the order:

const full_name = url.pathname.slice(1).replace(/\.git$/, '').replace(/\/+$/, '');

This ensures trailing slashes are removed after the .git suffix is handled.

Suggested change

	const full_name = url.pathname.slice(1).replace(/\/+$/, '').replace(/\.git$/, '');
	const full_name = url.pathname.slice(1).replace(/\.git$/, '').replace(/\/+$/, '');

[Copilot]

All errors in the try-catch block return a 404 status code, but not all errors represent "not found" scenarios. For example, if the URL parsing fails (line 47) or if it's not a GitHub URL (line 48-49), a 400 Bad Request would be more appropriate. Consider differentiating error types:

} catch (error) {
  if (error.response) {
    console.error("GitHub API error:", {
      status: error.response.status,
      message: error.response.data?.message,
      documentation_url: error.response.data?.documentation_url
    });
    res.status(404).json({ error: 'Repository not found or you do not have access.' });
  } else {
    console.error("Error adding repo:", error.message);
    res.status(400).json({ error: error.message });
  }
}

Suggested change

	if (error.response) {
	console.error("GitHub API error:", {
	status: error.response.status,
	message: error.response.data?.message,
	documentation_url: error.response.data?.documentation_url
	});
	} else {
	console.error("Error adding repo:", error.message);
	}
	res.status(404).json({ error: 'Repository not found or you do not have access.' });
	if (
	error instanceof TypeError || // Malformed URL
	error.message === 'Not a GitHub URL'
	) {
	console.error("Bad request error adding repo:", error.message);
	return res.status(400).json({ error: error.message });
	}
	if (error.response) {
	console.error("GitHub API error:", {
	status: error.response.status,
	message: error.response.data?.message,
	documentation_url: error.response.data?.documentation_url
	});
	if (error.response.status === 404) {
	return res.status(404).json({ error: 'Repository not found or you do not have access.' });
	} else if (error.response.status === 403) {
	return res.status(403).json({ error: 'Access to repository is forbidden.' });
	} else {
	return res.status(502).json({ error: 'Error communicating with GitHub API.' });
	}
	}
	console.error("Unexpected error adding repo:", error.message);
	res.status(500).json({ error: 'Internal server error.' });

[Copilot]

After this change, the unified and remark-parse packages are no longer used in the codebase. Consider removing them from package.json dependencies to reduce bundle size and maintenance overhead.