docs: clarify that plugin functionality is bundled, not managed by fisher

Only jorgebucaran/fisher itself is in fish_plugins. The functionality
from catppuccin/fish, fzf.fish, done, autopair, and puffer-fish is
bundled directly with this config in modified form and must not be
installed or updated via fisher.

Removes sponge (not present), corrects file path mappings for bundled
components, fixes stale "Plugin sync failed" message in first_run.fish,
and expands fish-config.index with missing sections 9–11.

docs/fish-config.md

@@ -279,7 +279,7 @@ are active in Insert, Normal, and Visual modes unless noted.
                     line to open an fzf picker and insert a selection
                     at the cursor position.
 
-## FZF Bindings (from PatrickF1/fzf.fish)
+## FZF Bindings (bundled from PatrickF1/fzf.fish)
 
     Ctrl+R          Search command history
     Ctrl+Alt+F      Search git-tracked files
@@ -1395,9 +1395,9 @@ To customize, override FZF_DEFAULT_OPTS in local.fish.
 
 ### Catppuccin Mocha Syntax Highlighting
 
-The catppuccin/fish plugin applies syntax highlight colors on first run.
-Colors are stored in fish_variables (universal). To switch variants, install
-a different theme from the themes/ directory:
+The Catppuccin Mocha theme ships with this config in themes/ and is applied
+on first run via `conf.d/first_run.fish`. Colors are stored in fish_variables
+(universal). To switch variants, install a different theme from themes/:
 
     fish_config theme save "Catppuccin Latte"
 
@@ -1417,18 +1417,33 @@ testing), run:
 
 Then open a new shell.
 
-The plugin list is maintained in fish_plugins at the config root.
+## Bundled Plugin Functionality
+
+Plugin functionality is bundled directly with this config rather than managed
+through Fisher. The bundled versions include customizations for Fish 4.x
+compatibility and improved behavior that differ from their upstream releases.
+Installing them through Fisher would overwrite these customizations.
+
+Bundled components and their upstream origins:
+
+    catppuccin/fish               → themes/ + conf.d/theme.fish
+    PatrickF1/fzf.fish            → functions/_fzf_*.fish + conf.d/fzf.fish
+    franciscolourenco/done        → conf.d/done.fish
+    jorgebucaran/autopair.fish    → functions/_autopair_*.fish + conf.d/autopair.fish
+    nickeb96/puffer-fish          → functions/_puffer_fish_*.fish + conf.d/puffer.fish
+
+Do not run `fisher install` for these — it will overwrite the customized
+versions. To update their behavior, edit the relevant bundled files directly.
+
+## fish_plugins Manifest
+
+The `fish_plugins` file at the config root contains only the Fisher manager
+entry itself:
 
     jorgebucaran/fisher           Plugin manager itself
-    catppuccin/fish               Catppuccin Mocha color theme
-    PatrickF1/fzf.fish            fzf integration for Fish
-    franciscolourenco/done        Desktop notification when long commands finish
-    jorgebucaran/autopair.fish    Auto-pair brackets and quotes
-    meaningful-ooo/sponge         Remove failed commands from history
-    nickeb96/puffer-fish          !! / !$ / ./ expansion
 
-Run `fisher update` to update all plugins, or `fish-deps update` which
-calls fisher update as its first step.
+To update Fisher, run `fisher update` or `fish-deps update` which calls it
+as its first step.
 
 ---
 
@@ -1439,8 +1454,9 @@ This configuration is managed as a git repository. To deploy on a new machine:
     mv ~/.config/fish ~/.config/fish.bak   # back up any existing config
     git clone https://git.rootiest.dev/rootiest/fish-config.git ~/.config/fish
 
-Then open a new Fish shell. Fisher and all plugins install automatically on
-first launch and the Catppuccin Mocha theme is applied.
+Then open a new Fish shell. Fisher installs automatically on first launch
+and the Catppuccin Mocha theme is applied. All other plugin functionality is
+bundled directly with this config and requires no additional installation.
 
 ## Return Sentinel