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feature: add api pdf processing (#506) * feat: add selectable paper parsers * fix: raw response text wrapper * fix: add missing import * fix: hide private metadata, group paper analysis configuration in cli * chore: group keys in cli * feat: add cli description for keys * chore: fix black formatting * chore: fix black formatting * test: remove redundant tests * fix: update parser test configuration * fix: address paper claims PR review comments * fix: solve test error
feat: add unified thesis repository analysis pipeline (#495) * feat: added thesis-analysis module * feat: add unified core thesis pipeline * chore: change default paper claims parameters * docs: update paper claims defaults * test: fix paper claims tests * fix: fix paper claims pipeline defaults * fix: solve thesis verification batches * refactor(repository-quality): rename formal VKR scorer * feat(thesis-analysis): add typed configuration and stage progress * feat(cli): expose analysis-only thesis and quality commands * refactor(repository-validation): remove obsolete validation * chore: fix black formatting * chore: black formatting * chore: fix black formatting * fix(thesis-verifier): validate results and read notebook context * fix(thesis-cli): isolate artifacts and stabilize progress output * feat: add independently owned thesis-analysis artifacts * feat: solve codex review comments * fix(focused-cli): protect clone cleanup and artifacts * fix(thesis-analysis): preflight claim sources and source fallback * fix(focused-cli): avoid artifact-default collisions * refactor(paper-analysis): replace thesis analysis contracts * feat(paper-analysis): make repository quality optional * test(paper-analysis): cover top-level entry point * docs(paper-analysis): document unified analysis workflow * chore: remove old thesis mentions * ci: bump tool to version 0.3.1 * fix: solve error with sourcecraft import * chore: solve black error
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