`get_readme` and `get_file_content` answered every failure with a string --
`[README not found: HTTP 404]`, `[File not found: HTTP 404]` -- while `main()`
prints any string result on stdout and exits 0. A rate-limited run, a missing
repository and a real README therefore arrived on the same channel with the same
exit code, so a caller reading stdout could not tell a failure from a body.
Both readers now raise `GitHubAPIError` naming the operation, the target and the
underlying HTTP error. The CLI's existing handler already writes an exception to
stderr and exits 1, so a failure leaves the success channel empty and the status
stays visible; a successful fetch is unchanged.
Pins both transports (requests and the urllib fallback), 404 against 403 so a
rate limit cannot read as a missing repository, the file reader's path, and the
CLI contract: non-zero exit, empty stdout, status on stderr.
* fix(github-research): resolve the tree against the repository's default branch
The tree command asked for "main" and, when that was missing, for "master".
A repository whose default branch is neither gets a name-guessing fallback, and
when the stale "master" still resolves GitHub returns it happily: the agent is
handed the tree of an abandoned branch and reports it as the current structure.
Ask for HEAD instead, which GitHub resolves to the repository's own default
branch, so no candidate names are guessed and no extra request is added.
* test(github-research): clarify stale branch tree comment
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
Preserve filename delimiters and literal percent escapes before either HTTP transport builds a Contents API request. Add offline regression coverage for requests and the urllib fallback.
* feat: Add github PAT configs, allowing larger github API rates.
* Update comment to English for better clarity
* fix: Remove unused config lines in config.example.yaml and unreferenced declarations in app_config. Fix lint issues and update documentation.
* fix: Remove unused imports, and passed the ruff check.
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* feat: add citation/reference support to deep research reports (#1141)
- Enhance lead agent system prompt with mandatory citation requirements
after web_search/web_fetch tool usage
- Add citation examples and best practices to GitHub Deep Research skill
- Add citation hints to report template (Executive Summary, Key Analysis)
- Style regular markdown links in frontend for visual distinction
(color, underline, hover effect)
- Fix TitleMiddleware being registered when title generation is disabled
* fix: address PR review comments
- Revert TitleMiddleware conditional registration (agent.py) to avoid
sync/async incompatibility with DeerFlowClient
- Fix markdown link rendering: merge classNames instead of overwriting,
only set target=_blank for external http(s) URLs
- Remove unrelated package.json/pnpm-lock.yaml changes
* fix: use plain markdown links in Sources section for cleaner rendering
Inline citations in report body use [citation:Title](URL) for pill/badge style.
Sources section uses plain [Title](URL) for simple underlined link style.
* fix(frontend): render plain links as underlined text in artifact markdown
Only links with citation: prefix render as Badge pills.
Regular links in Sources section now render as underlined text links.
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Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
