Release ViOTUcluster 0.6.0 with Conda-first install docs

[liusihang]

Summary

This PR brings the post-PR24 install/runtime follow-up work back to master and cuts the upstream 0.6.0 line.

Included

• switch the source install path to checked-in Conda environment manifests
• harden the validated main runtime and VirSorter2 database checks
• promote Bioconda/mamba installation as the preferred path in the README
• bump the packaged version to 0.6.0
• add docs and focused tests for the Conda/Bioconda release contract

Validation

Local:

• python3 -m unittest tests.test_shell_contracts tests.test_pipeline_orchestration_contract tests.test_installation_contract -v
• python3 -m py_compile ViOTUcluster/config.py

Remote on em:

• conda build .../recipes/viotucluster --no-test ... --croot /home/em/tmp/viotucluster-conda-bld-060
• conda create -p /home/em/tmp/viotucluster-pkgtest-env-060 --solver libmamba ... viotucluster=0.6.0
• ViOTUcluster --help
• ViOTUcluster_AllinOne --help
• python -c "import ViOTUcluster"

Notes

• Upstream release/tag already created: v0.6.0
• Bioconda draft PR updated to the matching source release: bioconda/bioconda-recipes#66783