Fix compiler warnings

[dbolser]

Summary

• fix sign-compare warnings in probability data parsing
• avoid sign mismatch in View
• use size_t for valueSize
• catch BGenError by reference
• document build/test steps in AGENTS.md

Testing

• ./waf configure
• ./waf
• ./build/test/unit/test_bgen
• ./build/apps/bgenix -g example/example.16bits.bgen -list

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https://chatgpt.com/codex/tasks/task_e_6888ce12e88c832786dcaec3bab9021f

[dbolser]

Closing this and its duplicate #2 for now, but recording what is on the branch, because it is worth reviving rather than losing.

A clean build of main (GCC 13.3, -Wall -pedantic) emits 45 warnings, 23 of them in code we own:

file	warnings
genfile/include/genfile/bgen/bgen.hpp	18 sign-compare
test/unit/test_variant_data_block.cpp	3 catch-value
src/View.cpp	1 sign-compare
apps/bgenix.cpp	1 sign-compare

This branch fixes every one of them, and the remaining 22 are boost, sqlite3 and zstd, which the -w hunks here silence. None of it has landed on main.

Notes for whoever picks it up:

• The hunks are indented with spaces in tab-indented files, so they read as whole-line rewrites rather than the small changes they are. Worth re-indenting before landing, as we did with the streampos fix.
• The bgen.hpp change touches the phased-parsing path in the public header. static_cast< uint32_t >( pack.numberOfAlleles ) - 1u makes explicit what the usual arithmetic conversions were already doing, so it is a warning fix rather than a behaviour change — but it deserves a careful look and a test run, since it is the one hunk in the core library.
• -w on the vendored wscripts is blunt, but defensible for code we do not maintain. It also silences sqlite3's known-benign -Wreturn-local-addr in sqlite3SelectNew.
• AGENTS.md predates the Python packaging and pytest suite, so it needs updating rather than restoring as-is.