docs: add obikmer user guide and MkDocs build configuration

Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.

UserDocMD/usage/utils.md

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+# utils
+
+Miscellaneous index maintenance and inspection utilities.
+
+```bash
+obikmer utils INDEXES... [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEXES...` | One or more index directories |
+
+## Options
+
+| Option | Scope | Description |
+|---|---|---|
+| `--new-label NEW=OLD` | single index only | Rename a genome label |
+| `--upgrade-index` | single index only | Add any missing layer metadata files to an older index |
+| `--bits-per-kmer` | single index only | Print bits-per-kmer statistics |
+| `--stats` | single index only | Print per-genome kmer counts as CSV |
+| `--partition-stats` | one or more indexes | Print a partition-size distribution report |
+| `--csv FILE` | with `--partition-stats` | Also write raw per-(partition, source) data to FILE as CSV |
+
+At least one operation option must be given. All options except `--partition-stats` require exactly one index directory.