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Workspace.checkpoint() called a nonexistent DirtyTracker.get_deleted() and passed arguments to the zero-arg CheckpointManager.create_checkpoint(), so every checkpoint raised and was silently swallowed by callers. It now uses deleted_files, forces a final stat-scan via the new scan_now(), and calls create_checkpoint() with its real signature.
DirtyTracker.scan_now(): force an immediate stat-scan diff so writes landing after the last poll tick (e.g. right before session close) are captured; no-op when a native watcher is active.
DirtyTracker now tracks workspace-root files. The workspace root is the agent's working directory, but only input/, working/, output/ were scanned, so files written at the root never synced.
FsspecSyncBackend: create parent directories before pipe in put_blob / put_manifest / put_checkpoint / publish_artifact — cloud filesystems create keys implicitly, but LocalFileSystem does not auto-create parent dirs, so blob/manifest/checkpoint writes to a file:// source raised FileNotFoundError.