Add xerxes codebase

[stschiff]

Draft Pull Request to add Xerxes codebase. Work in progress. To be merged into master after #351 has been fully merged.

[nevrome]

Thanks for starting this big integration! I think we could go to v2.0.0.0 when this is merged.

[stschiff]

OK amazingly this is finished with relatively minimal further changes needed. I suggest we keep this in draft stage until #351 is merged in. But one thing that we still need to do here is to adapt the github workflow for the release compilation. I took a brief look, and it seems more than a simple addition here or there, because now we need multiple executables to be built and added to a release. If you have capacity, @nevrome, please have a look. Otherwise I would try to adapt this with help of Chat-AI. Thanks.

[nevrome]

OK - great! It doesn't compile yet due to some syntax error, but we can look into this when we want to merge (after #351). For the moment thank you for preparing all of this! Must have been a good deal of work 🙏

[stschiff]

Really? Hmm, it compiled for me, I even tried xerxes... let me check again

[stschiff]

So, running stack clean and then stack build --pedantic works without problems for me, both on my Work Mac (Intel) and on my MacBook (Arm64)

[stschiff]

Ah wait... tests fail, and also stylish-haskell... I think I haven't tested the tests. Sorry for that. On it.

[stschiff]

All fixed.

[codecov]

Codecov Report

❌ Patch coverage is 32.44973% with 739 lines in your changes missing coverage. Please review.
✅ Project coverage is 51.71%. Comparing base (163a00f) to head (af9f43c).

Files with missing lines	Patch %	Lines
src/Poseidon/Analysis/CLI/FStats.hs	1.61%	305 Missing ⚠️
src/Poseidon/Analysis/FStatsConfig.hs	17.73%	112 Missing and 4 partials ⚠️
src/Poseidon/ColumnTypesJanno.hs	44.23%	38 Missing and 49 partials ⚠️
src/Poseidon/Janno.hs	62.02%	4 Missing and 56 partials ⚠️
src/Poseidon/Analysis/Utils.hs	38.96%	46 Missing and 1 partial ⚠️
src/Poseidon/SequencingSource.hs	46.03%	7 Missing and 27 partials ⚠️
src/Poseidon/CLI/OptparseApplicativeParsers.hs	0.00%	26 Missing ⚠️
src/Poseidon/ColumnTypesSSF.hs	37.14%	9 Missing and 13 partials ⚠️
src/Poseidon/Package.hs	57.77%	15 Missing and 4 partials ⚠️
src/Poseidon/CLI/Forge.hs	71.42%	6 Missing ⚠️
... and 7 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #369      +/-   ##
==========================================
- Coverage   56.98%   51.71%   -5.28%     
==========================================
  Files          33       36       +3     
  Lines        5052     5857     +805     
  Branches      549      642      +93     
==========================================
+ Hits         2879     3029     +150     
- Misses       1624     2186     +562     
- Partials      549      642      +93     

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