Bug fixes for RELION import

[MihinP]

Summary

This PR resolves RELION compatibility issues and fixes the Y-axis coordinate flip introduced by the denoiser, addressing #46, #47, and #48 (sub-issues of #44).

Closes #46
Closes #47
Closes #48
Closes #44

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Changes

Bug Fixes

Fixed: Y-axis coordinates flipped when using PartiNet denoise (#48)

• Removed erroneous .T (transpose) and np.rot90 operations from guided_denoiser.py that were causing micrograph Y-axis inversion
• Documentation updated to note that v1.0.0 users should enable Flip in y in CryoSPARC/RELION when extracting particles, and that this is no longer required in v1.0.1+

Fixed: STAR file format incompatible with RELION particle extraction (#46)

• Added RELION-compatible STAR file output to star_file.py
• New --relion flag generates a pick.star manifest and per-micrograph coordinate STAR files under <relion_project>/partinet/
• New --relion-project-dir and --mrc-prefix CLI options added to partinet star
• CryoSPARC output retained as default behaviour

Fixed: STAR file output uses Windows line endings (CRLF) (#47)

• Explicitly set newline="\n" and lineterminator="\n" on all STAR file writers in star_file.py to ensure Unix line endings (LF) regardless of host OS

Documentation

• Updated README.md, getting-started.md, intro.md, denoise.md, and star.md to reflect RELION output support and corrected descriptions
• Added version-specific warning in star.md for v1.0.0 Y-axis flip workaround