Misc. fixes and updates

[espenhgn]

Fixes #309
Fixes #311
Fixes #313

Changes proposed in this pull request:

• add library(bit64) to ldpred2.R to correctly read FID/IIDs that may be represented as 64-bit integers in .rds file
• disabled git LFS use in GH actions
• remove shapeit5 as main repo has been taken down w. DMCA notice

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  section of the CONTRIBUTING docs.
• I've updated or added any relevant documentation and docstrings where appropriate in the codebase.
• If this PR fixes a bug, I've added a test that will fail without my fix.
• If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.