docs(manual): document sub-categories in customization, reference index, and troubleshooting

Sub-categories were previously undocumented outside README and the
per-category reference pages. Add a paragraph to 07-customization.md (the
canonical opinionated-components page) explaining the sub-category cascade,
a short note to the 08-components-reference index pointing readers at each
category's sub-category list, and a troubleshooting note that
__fish_config_op_<category>_<subcategory> variables follow the same
check/reset pattern as category variables.

docs/manual/07-customization.md

@@ -145,6 +145,19 @@ NOTE:
   - Disabled integration commands (spwin, tab, split, hist, logs, upgrade) print an error naming the variable that disabled them.
   - On CachyOS, the distro fish config's own aliases, history override, and bang-bang bindings are stripped per category as well.
 
+### Sub-categories
+
+Each of the six categories further sub-divides into two to six
+sub-categories, each with its own `__fish_config_op_<category>_<subcategory>`
+variable (e.g. `__fish_config_op_aliases_filesystem`). These follow the
+exact same truthy/falsy/unset cascade one level deeper: an explicit
+sub-category value overrides the master switch and the parent category's
+setting, and an unset sub-category inherits from its parent category (which
+in turn inherits from `__fish_config_opinionated`). Run config-settings and
+press Enter on a category row to browse and toggle its sub-categories
+interactively. See [Components Reference](/08-components-reference/) for the
+full sub-category breakdown of every category.
+
 
 ## Prompt and Theme
 

docs/manual/08-components-reference/index.md

@@ -19,6 +19,10 @@ category variable.
     C5         [Logging and Capture](/08-components-reference/05-c5-logging-and-capture/) — Session logs, command duration
     C6         [Greeting & First-Run UI](/08-components-reference/06-c6-greeting-and-first-run-ui/) — Custom startup banner
 
+Each category further sub-divides into two to six sub-categories (24 in
+total) with their own `__fish_config_op_<category>_<subcategory>` toggles
+-- see that category's page for its sub-category list.
+
 ## Per-function overrides: `C0`/`always`
 
 Every guarded function or file can also carry a reserved `always/on` or

docs/manual/12-troubleshooting.md

@@ -237,6 +237,13 @@ Re-enable everything:
 
     set -Ue __fish_config_opinionated
 
+Each category also has two to six sub-categories (e.g.
+`__fish_config_op_aliases_filesystem`) that can be checked, disabled, or
+reset the same way — `set -U __fish_config_op_<category>_<subcategory> off`
+and `set -Ue __fish_config_op_<category>_<subcategory>` work identically to
+the category-level recipes above, just one level more granular. See
+[Components Reference](/08-components-reference/) for the full list.
+
 For an interactive alternative to setting these variables by hand, run `config-settings`.
 
 ---