Remove documentation for Kmer theory, phylogeny models, and usage examples

Documentation related to Kmer indexing, phylogeny models, and usage examples has been removed, retaining only the formats and architecture notes.

_Sidebar.md

@@ -4,36 +4,36 @@
 - [Installation](installation)
 ## Theory
 ### Kmer indexing
-    - [DNA encoding](theory-kmer_indexing-encoding)
-    - [Kmers](theory-kmer_indexing-kmers)
-    - [Minimizer selection](theory-kmer_indexing-minimizer_selection)
-    - [Super-kmers](theory-kmer_indexing-superkmers)
-    - [Partitioning and indexing architecture](theory-kmer_indexing-indexing_architecture)
-    - [Low-complexity kmer filter](theory-kmer_indexing-entropy_filter)
+- [DNA encoding](theory-kmer_indexing-encoding)
+- [Kmers](theory-kmer_indexing-kmers)
+- [Minimizer selection](theory-kmer_indexing-minimizer_selection)
+- [Super-kmers](theory-kmer_indexing-superkmers)
+- [Partitioning and indexing architecture](theory-kmer_indexing-indexing_architecture)
+- [Low-complexity kmer filter](theory-kmer_indexing-entropy_filter)
 ### Phylogeny
 #### Kmer-based
-      - [Distance metrics](theory-phylogeny-kmer_based-distance_metrics)
+- [Distance metrics](theory-phylogeny-kmer_based-distance_metrics)
 #### SNP-based
-      - [Central-position SNP model](theory-phylogeny-snp_based-central_snp_model)
-      - [Gamma rate heterogeneity](theory-phylogeny-snp_based-gamma_rate_heterogeneity)
-      - [Sankoff model](theory-phylogeny-snp_based-sankoff_model)
-      - [Sampling design](theory-phylogeny-snp_based-sampling_design)
+- [Central-position SNP model](theory-phylogeny-snp_based-central_snp_model)
+- [Gamma rate heterogeneity](theory-phylogeny-snp_based-gamma_rate_heterogeneity)
+- [Sankoff model](theory-phylogeny-snp_based-sankoff_model)
+- [Sampling design](theory-phylogeny-snp_based-sampling_design)
 ## Usage
-  - [superkmer](usage-superkmer)
-  - [index](usage-index_command)
-  - [merge](usage-merge)
-  - [filter](usage-filter)
-  - [select](usage-select)
-  - [query](usage-query)
-  - [dump](usage-dump)
-  - [annotate](usage-annotate)
-  - [phylo](usage-phylo)
-  - [unitig](usage-unitig)
-  - [estimate](usage-estimate)
-  - [convert](usage-convert)
-  - [utils](usage-utils)
-  - [pack](usage-pack)
-  - [Predicates and taxonomy paths](usage-predicates)
+- [superkmer](usage-superkmer)
+- [index](usage-index_command)
+- [merge](usage-merge)
+- [filter](usage-filter)
+- [select](usage-select)
+- [query](usage-query)
+- [dump](usage-dump)
+- [annotate](usage-annotate)
+- [phylo](usage-phylo)
+- [unitig](usage-unitig)
+- [estimate](usage-estimate)
+- [convert](usage-convert)
+- [utils](usage-utils)
+- [pack](usage-pack)
+- [Predicates and taxonomy paths](usage-predicates)
 ## Formats
-  - [Index construction and on-disk layout](formats-index_layout)
+- [Index construction and on-disk layout](formats-index_layout)
 - [Architecture notes](architecture)