Fix three agent bugs found in the v2 runs

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HighnessAtharvayesterday
  1. A piped install with no curl passed falsely, because the pipe took bash's exit code. Every step now runs with set -o pipefail.
  2. Recovery read pip progress lines as the error and kept the wrong class on later attempts. It now strips package-manager noise and reads stderr last.
  3. A fix that only installs system packages counted as a docs bug and produced an apt-get line in the docs diff. It now counts as an environment fix, which stays out of the docs.

Entire-Checkpoint: 01M4JHKWA5FYWHHKN8CWRNFSME

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