echoverse: Break up echolocatoR into sub-packages

[bschilder]

This will make it more modular and easier to debug.

Proposed modules:

• echolocatoR (echoverse branch): Core functions such as workflow and utilities.
• echofinemap: Fine-mapping functions.
• echoLD: LD downloading and processing (UKB, 1KG).
• echoAI: API access to variant-level AI predictions (IMPACT, DeepSEA, SpliceAI).
• echoannot: API access to variant-level epigenomic/genomic annotations (XGR, Roadmap, ENCODE).
• echotabix: Tabix-indexing of tabular and vcf files.
• echopeaks: Peak calling (MACS2). Now integrated into echoannot, with additional functionality available via PeakyFinders
• echovalidate: Validation functions such as annotation enrichment with bootstrapping.
• echoconda: Conda env utility functions.
• catalogueR: eQTL Catalogue API and colocalization.
• downloadR: Single- or multi-threaded downloading functions.
• ggLocusZoom: Locus plotting. Replaced by echoplot.
• echoplot: Locus plotting (replacement for ggLocusZoom).
• echodata: Fine-mapping results, echolocatoR Fine-mapping Portal API, and related datasets.
• echogithub: Extract data and metadata from GitHub

Extra modules

• echoverseTemplate: template for echoverse subpackages.
• echodeps: Create dependency graphs from R packages.