Several bug fixes

[taylorbell57]

This PR:

• Makes minor cosmetic changes to several log statements
• Removes the h5py upper limit which is no longer needed and breaks python>3.9 installs
• Avoids over-writing ypos and ywidth plots (figs 3104 & 3105) when there are multiple segments (resolves #528)
• Resolves #537 by removing the bug-inducing and unnecessary wave_1d_trimmed variable
• Resolves #521 by moving the self.superbias = Eureka_SuperBiasStep() line earlier
• Resolves #501 by reshaping ld_coeffs for for input LD files for white lightcurves.
• Makes progress on #540, but we should still add documentation about exotic-ld on the installation instructions page
• Resolves #531 by further clarifying the manual_clip index convention
• Resolves #476 by helping users understand how to get access to longer or shorter wavelengths in S4 if they are outside of the current wavelength range.
• Resolves #483 by using the built-in shlex package to preserve spaces in quoted substrings since some people put spaces in their folder names.

[codecov-commenter]

Codecov Report

Merging #539 (d2eecbf) into main (43c4a23) will decrease coverage by 0.01%. The diff coverage is 46.34%.

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@@            Coverage Diff             @@
##             main     #539      +/-   ##
==========================================
- Coverage   57.52%   57.51%   -0.01%     
==========================================
  Files          92       92              
  Lines       11127    11137      +10     
==========================================
+ Hits         6401     6406       +5     
- Misses       4726     4731       +5     

Impacted Files	Coverage Δ
src/eureka/S1_detector_processing/bias_sub.py	12.19% <0.00%> (-0.16%)	:arrow_down:
src/eureka/S1_detector_processing/group_level.py	8.33% <0.00%> (-0.09%)	:arrow_down:
src/eureka/S1_detector_processing/s1_process.py	13.59% <0.00%> (ø)
...eureka/S1_detector_processing/update_saturation.py	6.25% <0.00%> (ø)
src/eureka/S4_generate_lightcurves/generate_LD.py	8.33% <0.00%> (-2.99%)	:arrow_down:
src/eureka/S5_lightcurve_fitting/s5_fit.py	67.06% <0.00%> (-0.66%)	:arrow_down:
src/eureka/S4_generate_lightcurves/s4_genLC.py	85.49% <77.77%> (-0.45%)	:arrow_down:
src/eureka/S3_data_reduction/plots_s3.py	68.66% <100.00%> (+0.10%)	:arrow_up:
src/eureka/S3_data_reduction/s3_reduce.py	87.84% <100.00%> (ø)
src/eureka/S6_planet_spectra/s6_spectra.py	49.53% <100.00%> (ø)
... and 1 more

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