Tianyi Cui 1167ea71b7 Merge latest master through rfc/pty into feature/persistent-pty-sessions ...

# Conflicts:
#	docs/module-graph.md

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..

input.json

feat: add persistent PTY sessions

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session.jsonl

Merge latest master through rfc/pty into feature/persistent-pty-sessions

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stdout.expected.jsonl

Merge latest master through rfc/pty into feature/persistent-pty-sessions

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system-prompt.expected.md

Merge latest master through rfc/pty into feature/persistent-pty-sessions

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tool-schemas.expected.json

Merge refreshed rfc/pty into feature/persistent-pty-sessions

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