Add fix for collect matched annotations

[klei22]

This pull request improves how whitespace is handled when writing output files in collect_matched_annotations.py, particularly to avoid stripping meaningful spaces from the param_nesting field. It also introduces a guardrail to detect accidental whitespace modifications, ensuring the integrity of the output.

Whitespace handling and output writing improvements:

• Updated write_concat to avoid using .rstrip() (which strips spaces) and instead only trim trailing newlines, preserving meaningful spaces in param_nesting.
• Refactored write_mc_inputs to use a new emit helper function that carefully strips only trailing newlines, and added a guardrail that raises an error if the output lengths for different fields do not match—helping catch accidental whitespace loss.

Other:

• Minor formatting adjustment at the end of the file.

[Copilot]

Pull request overview

This PR adjusts output serialization in collect_matched_annotations.py to preserve meaningful trailing spaces (notably in param_nesting) while still normalizing trailing newlines, and adds a guardrail to detect unexpected whitespace/length divergence across the three aligned annotation streams.

Changes:

• Updated write_concat to avoid .rstrip() and only remove trailing \n before writing.
• Refactored write_mc_inputs to centralize newline-only trimming via an emit() helper.
• Added a length-consistency guardrail across emitted mc_out, mc_pna, and mc_ga inputs.

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