CI: Update populate-depot to latest version

• populate-depot: Silence mypy warnings

  (originally steamlinuxruntime@0c0e1b3a)

• populate-depot: Improve version logging

  (originally steamlinuxruntime@13ae83de)

• populate-depot: Add use_tool_subprocess_reaper flag

  (originally steamlinuxruntime@fa634281)

• populate-depot: Assume pressure-vessel-wrap unpacks runtimes

  (originally steamlinuxruntime@3f821430)

• populate-depot: Take source files from separate directories

  This avoids the depot being a mixture of source files and generated files.

  (originally steamlinuxruntime@f36fbcda)

• CI: Adjust populate-depot invocation for latest version

  The latest version in SteamLinuxRuntime requires a ${source_dir}/common directory available.