ASA calculation performance tweaks - #1148
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Replaces IndexAndDistance object arrays with primitive int[] and double[] arrays in a Neighbors holder, sorted at creation time to eliminate per-atom sort calls and reduce object allocations.
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Covers what is merged since 7.2.6 and what is open and expected to land: the download and checksum work, the CATH and ECOD fixes, the contact and ASA performance tweaks, electron density, and the JUnit 5 migration. Five entries are for pull requests that are still open - biojava#1134, biojava#1147, biojava#1148, biojava#1150 and biojava#1151 - and should be checked against what actually merged before the release is tagged.
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The runtime gain should be around 1.2-1.3x. And together with #1147 it is about 1.3-1.5x
Implemented by Claude and fully tested. Output is identical to the previous implementation.
The changes are to replace objects with flat primitive arrays so the hot loops are sequential scans over contiguous memory instead of pointer chases.