Prepare 0.4.0 structure input release

[galjos]

Summary

• promote read_structure(...) to the primary public structure reader and keep restart and XYZ parsing behind one API
• rename the CLI surface to structure and make XYZ plus moldescriptor compatibility explicit
• add CLI coverage for XYZ input, add a short changelog entry, and bump package metadata to 0.4.0

Why

This turns the recent XYZ support into a coherent minor release instead of a patch-level feature add. The public input model is now structure-oriented rather than restart-oriented, and the ambiguous XYZ plus multi-molecule moldescriptor path fails explicitly.

Validation

• /Users/jog/.juliaup/bin/julia --project=. --color=yes -e "import Pkg; Pkg.test()"
• /Users/jog/.juliaup/bin/julia --project=docs --color=yes docs/make.jl

[codecov]

Codecov Report

❌ Patch coverage is 94.73684% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.15%. Comparing base (bf9f405) to head (10ba10c).

Files with missing lines	Patch %	Lines
src/read_files.jl	94.73%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #33      +/-   ##
==========================================
+ Coverage   95.09%   96.15%   +1.06%     
==========================================
  Files           8        8              
  Lines         326      338      +12     
==========================================
+ Hits          310      325      +15     
+ Misses         16       13       -3     

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