Cline's apply_patch was silently destroying files when a model used "Add File" on an existing path

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Cline v4.1.19 fixes `apply_patch` silently overwriting an existing file when the model issues an "Add File" operation on a path that already exists; the contents were replaced with no error and no record of what was lost. The release also fixes `run_commands` hanging until its timeout after a command that backgrounds a child process holding the output pipes open, and reports commands that succeed with no output (`git add -A` on a clean tree) as empty rather than as a shell-integration failure that fed the model unrelated terminal scrollback.