fix: use error estimation config in levels contexts

[singjc]

This pull request updates how error estimation parameters are accessed in the infer_glycopeptides function, improving code organization and maintainability by grouping related configuration values under error_estimation_config.

Configuration refactoring:

• Updated the function call in levels_contexts.py so that error estimation parameters (such as parametric, pfdr, pi0_lambda, etc.) are now accessed via config.error_estimation_config instead of directly from config. This centralizes error estimation settings and makes the codebase easier to manage.

[Copilot]

Pull request overview

This pull request refactors infer_glycopeptides to consistently read error-estimation parameters from the nested config.error_estimation_config, aligning glycopeptide-level inference with the rest of the level-context workflows and centralizing error-estimation settings.

Changes:

• Updated the glycopeptide (global / experiment-wide) inference path to pass error-estimation parameters via config.error_estimation_config.* instead of config.*.
• Keeps the glycopeptide inference API the same while making configuration usage consistent and easier to maintain.

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