Update wiki to reflect current software state
- Home: remove conduit-basecamp/conduit-summit refs, add Conduit-GUI, update method list
- Getting-Started: fix output paths (runs/{run_name}/), add run_name requirement, fix input file formats
- Workflow-Architecture: update directory tree, add module dependency table, fix output paths
- Search-Space: fix all method names (ncbi_taxonomy_id, uniprot_proteome_id, peptidotyping, MAGs), remove unsupported 16S, add uniprot_proteome_id section, fix ncbi_taxa_ids.txt format
- Dependancy-Management: fix duplicate Windows heading (second was macOS), add unsupported platform notes
- Conduit-Object: replace conduit-summit with Conduit-GUI
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Updated Search Space (markdown)
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