Fail fast on check runtime directory errors

[codeforester]

Summary

• Treat empty JSON output from failed Python check/profile layers as fatal pre-output failures.
• Preserve normal structured project/profile diagnostics when those layers return JSON with an error status.
• Add a shell regression for runtime-dir failures that must emit only the concise Python error.

Validation

• env BASE_BASH_LIBS_DIR=/Users/rameshhp/work/base-bash-libs/lib/bash bats cli/bash/commands/basectl/tests/check.bats --filter "basectl check project --format json fails fast on runtime directory errors"
• env BASE_BASH_LIBS_DIR=/Users/rameshhp/work/base-bash-libs/lib/bash bats cli/bash/commands/basectl/tests/check.bats
• env -u BASE_HOME BASE_BASH_LIBS_DIR=/Users/rameshhp/work/base-bash-libs/lib/bash ./bin/base-test
• git diff --check

Fixes #910