chore(skill): scaffold molecule and atom files

paperforge/skills/paperforge/atoms/clarify-user-intent.md

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+# clarify-user-intent
+
+Clarify the user's intent before dispatching to a skill workflow.

paperforge/skills/paperforge/atoms/extract-methodology-card.md

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+# extract-methodology-card
+
+Extract a structured methodology card from a paper.

paperforge/skills/paperforge/atoms/retrieval-routing.md

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+# retrieval-routing
+
+Route between vector and memory retrievers based on query type.

paperforge/skills/paperforge/atoms/write-project-log.md

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+# write-project-log
+
+Write a general project log entry.

paperforge/skills/paperforge/atoms/write-project-reading-log.md

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+# write-project-reading-log
+
+Write a formatted reading log entry to the project README.

paperforge/skills/paperforge/atoms/write-reading-log-jsonl.md

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+# write-reading-log-jsonl
+
+Append a structured reading entry to the JSONL reading log.

paperforge/skills/paperforge/molecules/capture-project-knowledge.md

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+# capture-project-knowledge
+
+Capture and persist knowledge gained from reading into project memory.

paperforge/skills/paperforge/molecules/deep-analyze-paper.md

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+# deep-analyze-paper
+
+Perform deep structural and methodological analysis of a paper.

paperforge/skills/paperforge/molecules/discover-papers.md

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+# discover-papers
+
+Search for and discover new papers relevant to the project.

paperforge/skills/paperforge/molecules/find-supporting-evidence.md

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+# find-supporting-evidence
+
+Find evidence to support a specific claim or question.

paperforge/skills/paperforge/molecules/read-known-paper.md

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+# read-known-paper
+
+Locate and interactively read a single known paper.