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fix: upgrade dependencies to resolve Dependabot security alerts#111

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fix/dependabot-security-alerts
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fix: upgrade dependencies to resolve Dependabot security alerts#111
gkorland wants to merge 1 commit intostagingfrom
fix/dependabot-security-alerts

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Summary

Upgrades vulnerable dependencies to resolve open Dependabot security alerts.

Updated packages

Package Before After Severity CVE/Issue
flask 3.1.2 3.1.3 Low Session Vary: Cookie header fix
werkzeug 3.1.5 3.1.6 Medium safe_join() Windows device names
pypdf 5.9.0 6.7.2 Medium Multiple DoS/infinite loop fixes
requests 2.32.3 2.32.5 Medium .netrc credential leak
graphrag-sdk 0.8.1 0.8.2 Minor update

Notes

  • pypdf and requests required [tool.uv] override-dependencies because upstream packages pin them:
    • graphrag-sdk pins pypdf<6.0.0
    • multilspy pins requests==2.32.3
  • The pypdf 5→6 major bump is safe — graphrag-sdk only uses PdfReader.extract_text(), which is unchanged.
  • urllib3 (2.6.3) and filelock (3.20.3) were already at patched versions.

Resolves Dependabot alerts: #85, #87, #89, #91, #92, #93, #94, #95, #96, #97, #98, #99, #100, #101, #102, #103, #104, #105, #106, #107, #108, #109, #110, #111, #112, #113

- flask 3.1.2 → 3.1.3 (session Vary: Cookie header fix)
- werkzeug 3.1.5 → 3.1.6 (safe_join Windows device names fix)
- pypdf 5.9.0 → 6.7.2 (multiple DoS/infinite loop fixes)
- requests 2.32.3 → 2.32.5 (.netrc credential leak fix)
- graphrag-sdk 0.8.1 → 0.8.2

Added uv override-dependencies for requests and pypdf to bypass
upstream constraints in multilspy (==2.32.3) and graphrag-sdk (<6.0.0).

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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