Genome-wide TWAS fixes: conversion edge cases, noResult for empty LD blocks, optional gene unit and CV prefilter - #1439

gwas_sumstats_construct.R writes no GwasSumStats file for a block without GWAS variants, so twas.R failed on readRDS and the whole region errored. Such genes now get an empty result with a noResult attribute.

twas_manifest.R gains --unit gene (one unit per gene spanning its weight window, so GWAS and LD are read per gene) next to the existing region grouping, which stays the script default. An optional CV prefilter (--min-cv-rsq / --max-cv-pval) skips genes where no context/method passes, so their GWAS input is never built; weights without per-row CV results are kept for pecotmr to decide. twas_ctwas.ipynb uses the gene unit and the prefilter by default (--twas_unit, --twas_prefilter).

- twas_ctwas.ipynb keeps region as the default TWAS unit, so existing commands give the same outputs; the gene unit is opt-in with --twas_unit gene.
- CV prefilter: off by default in the notebook (--twas_prefilter turns it on for twas runs), since the ctwas steps read the same manifest and cTWAS uses every gene with weights. It now reads the per-method CV results of the pecotmr 0.9.5+ TwasWeights layout (it previously found no metrics there and kept every gene), ignores methods without a CV r2 such as ensemble, uses the twas step's --rsq-option and --rsq-pval-option, keeps genes with no CV metrics, no cvResult column or an unreadable weight file (reported on stderr), treats --min-cv-rsq <= 0 as off, and loads pecotmr before reading the weights.
- Gene unit: make region_id file-name safe and stop when the xQTL meta repeats a gene, since both would collide on output paths.
- twas_weights_conversion.R: skip all-zero/NA weights before resolving variant IDs, and prefer preset_variants_result IDs when their length fits.
- Tests: the notebook twas test pins the region unit; new tests cover the gene unit (same result as the region unit on the toy gene), gene-unit manifest rows, repeated genes, and the prefilter keep/drop rules.

- twas_manifest.R: --unit gene stops early when a gene has no start/end in the xQTL meta, checks for repeated genes before making IDs file-name safe, and stops when two genes would share a file name. The CV prefilter skips cvResult entries that are not lists instead of reporting the file as unreadable.
- twas.R: a missing GwasSumStats file still means an empty window, but a missing folder now stops as a wrong path; the noResult text no longer assumes an LD block.
- twas_ctwas.ipynb: the twas step removes an old GwasSumStats file before rebuilding it, makes the gene part of output names file-name safe, and the Input and Command Interface sections list --twas_unit, --twas_prefilter, --rsq_option and --rsq_pval_option.
- twas_weights_conversion.R: report genes without usable weights with message(), since the warning was lost on quit().
- Tests: prefilter p-value cutoff (keep and drop, with the pval fall-back and ensemble skip), NA gene window, file-name safe IDs and clashes, missing GwasSumStats file and folder, and conversion of weights without names, with unmatched IDs and with all-zero weights.