Optimize PeptideIndexer

[cbielow]

Description

This PR removes the costly storage of all peptide hits in a std::map and uses std::vector instead.
Also each hit takes up less space now.

For an (extreme) dataset with 1e9 hits (!), the runtime reduces from 1h to 15min, while the peak memory usage reduces from 134 GB to 91 GB. The resulting idXML is 34 GB in size.

There is further potential (since there is another map) but that is for another PR.

This change also surfaced a small bug in the new AC implementation (#5776), which may report hits twice (which was not discovered since the results were stored in a map). This is also fixed now.

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[jpfeuffer]

Suggested change

	Hit::T peptide_index; ///< index of the peptide
	Hit::T peptide_index; //< index of the peptide

[cbielow]

documenting members is done with ///< ...., so I guess it would be better to fix the other two members as well?
https://www.doxygen.nl/manual/docblocks.html#memberdoc

[jpfeuffer]

with minor doc suggestions

[cbielow]

apply suggestions from review