PR-1: Hydra-Powered YAML Configuration and run as Pip module

[YaoYinYing]

This is one of the separated PRs from #321 .

Full PR roadmap

id	purpose	# commits	Affected
1	Hydra-Omegaconf and Pip module	6	Code, Config, Doc
2	BFD supports and MSA parallelism fixes	5	Code, Config, Case
3	Small molecule inputs and covalent bonds	4	Code, Case, Doc

Changelog:

Added

• Configurability via YAML, supported by Hydra and OmegaConf.
• New helixfold run command for performing inference.

Changed

• Transitioned HelixFold3 to a pip-installable package.
• Overrides now handled through CONFIG_DIFFS.
• Replaced ml_collections.ConfigDict with DictConfig for better integration.

Fixed

• Implemented automatic binary search within the PATH if not explicitly specified.

Removed

• Deprecated requirements.txt in favor of direct pip installation dependencies.
• Removed run_infer.sh script as functionality is now integrated into the main command interface.

[RyanGarciaLI]

@YaoYinYing It looks good to start, but it still needs further improvement. You can add my WeChat id "******", and we can discuss more details.

[CLAassistant]

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❌ RyanGarciaLI
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