docs: fix formatting and links in troubleshooting

Converted plain text references to Markdown links across the troubleshooting documentation and index.md. Converted commands to properly formatted inline code blocks, and ensured code blocks conform to the SSOT's indented-block requirements.

docs/fish-config.md

@@ -47,7 +47,7 @@ output, file contents, and secrets printed to the terminal. Nothing leaves
 your machine, but the files persist locally.
 - Disable all logging with: `set -U __fish_config_op_logging off`
 - Prefer a menu? Run the interactive picker: `config-settings`
-- See Section 7 (C5 - Logging and Capture) for the full breakdown.
+- See [C5 — Logging and Capture](/07-customization/#c5--logging-and-capture) for the full breakdown.
 
 The configuration uses a structured file tree:
 
@@ -3214,7 +3214,7 @@ Re-enable:
 
     set -Ue __fish_config_op_logging
 
-See Section 7, "C5 — Logging and Capture" for the full component breakdown.
+See [C5 — Logging and Capture](/07-customization/#c5--logging-and-capture) for the full component breakdown.
 
 ## Change or Disable the Greeting
 
@@ -3235,7 +3235,7 @@ testing):
 
     set -Ue __fish_config_first_run_complete
 
-See Section 7, "C6 — Greeting and First-Run UI" for details.
+See [C6 — Greeting and First-Run UI](/07-customization/#c6--greeting-and-first-run-ui) for details.
 
 ## Secrets and Machine-Local Configuration
 
@@ -3259,7 +3259,7 @@ Disable it with:
 
     set -U __fish_user_dots_symlink false
 
-See Section 10, "Personalization" for the full local.fish / secrets.fish
+See [Personalization](/10-personalization/) for the full `local.fish` / `secrets.fish`
 layout.
 
 ## Tool Init Does Nothing (Return Sentinel)
@@ -3267,16 +3267,16 @@ layout.
 Symptom: you ran a tool's setup command (e.g.
 `starship init fish >> ~/.config/fish/config.fish`) and nothing changed.
 
-Cause: config.fish ends with a `return` guard. Any lines appended after it
+Cause: `config.fish` ends with a `return` guard. Any lines appended after it
 are never executed.
 
-Fix: create a dedicated conf.d file instead of appending to config.fish:
+Fix: create a dedicated `conf.d/` file instead of appending to `config.fish`:
 
     # ~/.config/fish/conf.d/mytool.fish
     mytool init fish | source
 
-All existing integrations (starship, zoxide, direnv) already have conf.d/
-files. See Section 9, "Return Sentinel" for background.
+All existing integrations (starship, zoxide, direnv) already have `conf.d/`
+files. See [Return Sentinel](/09-installation/#return-sentinel) for background.
 
 ## Missing Dependencies
 
@@ -3299,16 +3299,16 @@ Or install everything missing and update what is installed:
 
     fish-deps sync
 
-See Section 6, "Dependency Catalog" for the full list grouped by tier
+See [Dependency Catalog](/06-dependency-catalog/) for the full list grouped by tier
 (required, integrations, recommended).
 
 ## Vi Mode Keybindings
 
 This config enables Vi mode by default (via C3 overrides), replacing the
 standard Emacs-style bindings. If Vi mode interferes with your workflow,
-override it in local.fish:
+override it in `local.fish`:
 
-    # in $__fish_user_dots_path/local.fish
+    # $__fish_user_dots_path/local.fish
     fish_default_key_bindings
 
 This restores Emacs-style bindings without disabling the rest of C3
@@ -3319,7 +3319,7 @@ overrides):
 
     set -U __fish_config_op_overrides off
 
-See Section 7, "C3 — Key and Environment Overrides" for the full list of
+See [C3 — Key and Environment Overrides](/07-customization/#c3--key-and-environment-overrides) for the full list of
 what C3 controls.
 
 ## Minimal Mode / Disabling Opinionated Features
@@ -3352,7 +3352,7 @@ Re-enable everything:
 
 Or use the interactive TUI: `config-settings`.
 
-See Section 7, "Opinionated Components (Minimal Mode)" for the full
+See [Opinionated Components (Minimal Mode)](/07-customization/#opinionated-components-minimal-mode) for the full
 component reference tables.
 
 ---

docs/manual/11-troubleshooting.md

@@ -91,7 +91,7 @@ Re-enable:
 
     set -Ue __fish_config_op_logging
 
-See Section 7, "C5 — Logging and Capture" for the full component breakdown.
+See [C5 — Logging and Capture](/07-customization/#c5--logging-and-capture) for the full component breakdown.
 
 ## Change or Disable the Greeting
 
@@ -112,7 +112,7 @@ testing):
 
     set -Ue __fish_config_first_run_complete
 
-See Section 7, "C6 — Greeting and First-Run UI" for details.
+See [C6 — Greeting and First-Run UI](/07-customization/#c6--greeting-and-first-run-ui) for details.
 
 ## Secrets and Machine-Local Configuration
 
@@ -136,7 +136,7 @@ Disable it with:
 
     set -U __fish_user_dots_symlink false
 
-See Section 10, "Personalization" for the full local.fish / secrets.fish
+See [Personalization](/10-personalization/) for the full `local.fish` / `secrets.fish`
 layout.
 
 ## Tool Init Does Nothing (Return Sentinel)
@@ -144,16 +144,16 @@ layout.
 Symptom: you ran a tool's setup command (e.g.
 `starship init fish >> ~/.config/fish/config.fish`) and nothing changed.
 
-Cause: config.fish ends with a `return` guard. Any lines appended after it
+Cause: `config.fish` ends with a `return` guard. Any lines appended after it
 are never executed.
 
-Fix: create a dedicated conf.d file instead of appending to config.fish:
+Fix: create a dedicated `conf.d/` file instead of appending to `config.fish`:
 
     # ~/.config/fish/conf.d/mytool.fish
     mytool init fish | source
 
-All existing integrations (starship, zoxide, direnv) already have conf.d/
-files. See Section 9, "Return Sentinel" for background.
+All existing integrations (starship, zoxide, direnv) already have `conf.d/`
+files. See [Return Sentinel](/09-installation/#return-sentinel) for background.
 
 ## Missing Dependencies
 
@@ -176,16 +176,16 @@ Or install everything missing and update what is installed:
 
     fish-deps sync
 
-See Section 6, "Dependency Catalog" for the full list grouped by tier
+See [Dependency Catalog](/06-dependency-catalog/) for the full list grouped by tier
 (required, integrations, recommended).
 
 ## Vi Mode Keybindings
 
 This config enables Vi mode by default (via C3 overrides), replacing the
 standard Emacs-style bindings. If Vi mode interferes with your workflow,
-override it in local.fish:
+override it in `local.fish`:
 
-    # in $__fish_user_dots_path/local.fish
+    # $__fish_user_dots_path/local.fish
     fish_default_key_bindings
 
 This restores Emacs-style bindings without disabling the rest of C3
@@ -196,7 +196,7 @@ overrides):
 
     set -U __fish_config_op_overrides off
 
-See Section 7, "C3 — Key and Environment Overrides" for the full list of
+See [C3 — Key and Environment Overrides](/07-customization/#c3--key-and-environment-overrides) for the full list of
 what C3 controls.
 
 ## Minimal Mode / Disabling Opinionated Features
@@ -229,7 +229,7 @@ Re-enable everything:
 
 Or use the interactive TUI: `config-settings`.
 
-See Section 7, "Opinionated Components (Minimal Mode)" for the full
+See [Opinionated Components (Minimal Mode)](/07-customization/#opinionated-components-minimal-mode) for the full
 component reference tables.
 
 ---

docs/manual/index.md

@@ -35,7 +35,7 @@ output, file contents, and secrets printed to the terminal. Nothing leaves
 your machine, but the files persist locally.
 - Disable all logging with: `set -U __fish_config_op_logging off`
 - Prefer a menu? Run the interactive picker: `config-settings`
-- See Section 7 (C5 - Logging and Capture) for the full breakdown.
+- See [C5 — Logging and Capture](/07-customization/#c5--logging-and-capture) for the full breakdown.
 
 The configuration uses a structured file tree: