docs(index): expand help-index coverage and fix stale targets

Add tool-name synonyms whose names appear in no heading (so the
fallback substring scan can't reach them): eza/exa/lsd, trash, btop,
prettyping, duf/dust, kitten, bat. Add integration and topic keywords
(zoxide, direnv, venv/virtualenv, wakatime, tailscale, done/notify,
pager-hierarchy, shell-aliases, kitty-logging/watcher, agy,
antigravity-ide, html/browser, wiki).

Fix stale entries pointing at renamed/removed headings:
- antigravity -> ### antigravity-resume (### antigravity was removed)
- man-page/manpage -> ## As a man page (dropped '(if compiled)')
- disambiguate duplicate 'secrets' key: secrets.fish is now secrets-file

docs/fish-config.index

@@ -133,7 +133,9 @@ logging=## 5.11 Pager and Logging
 logs=### logs
 smart-exit=### smart_exit
 ai=## 5.12 AI and Developer Tools
-antigravity=### antigravity
+antigravity=### antigravity-resume
+antigravity-ide=### antigravity-ide
+agy=### agy
 claude-cli=### claude
 claude=### claude-resume
 claude-docs=### claude-docs
@@ -156,6 +158,37 @@ replay=### replay
 tmux=### tmux-clean
 wake-lock=### wake-lock
 
+# ── Tool-name synonyms (replacement → shadowed command) ──────
+# These tools don't appear in any heading, so the fallback scan can't
+# find them; map each to the function that wraps it.
+eza=### ls
+exa=### ls
+lsd=### ls
+trash=### rm
+btop=### top
+prettyping=### ping
+duf=### du
+dust=### du
+kitten=### ssh
+bat=### cat
+
+# ── Tool integrations (Section: Integrations) ────────────────
+zoxide=### Zoxide
+z=### Zoxide
+direnv=### DirEnv
+venv=### Auto Python Venv
+virtualenv=### Auto Python Venv
+python=### Auto Python Venv
+wakatime=### WakaTime
+tailscale=### Tailscale
+done=### Done Notifications
+notifications=### Done Notifications
+notify=### Done Notifications
+pager-hierarchy=## Pager Hierarchy
+shell-aliases=## 4.11 Shell Aliases
+kitty-logging=### kitty-logging
+watcher=### kitty-logging
+
 # ── Section 6: Dependency Catalog ────────────────────────────
 catalog=# 6. DEPENDENCY CATALOG
 deps-catalog=# 6. DEPENDENCY CATALOG
@@ -229,13 +262,16 @@ updating=## Updating
 # ── Section 10: Personalization ───────────────────────────────
 personalization=# 10. PERSONALIZATION
 personalize=# 10. PERSONALIZATION
-secrets=## secrets.fish
+secrets-file=## secrets.fish
 local-config=## local.fish
 
 # ── Section 11: Viewing This Manual ──────────────────────────
 viewing=# 11. VIEWING THIS MANUAL
 manual=# 11. VIEWING THIS MANUAL
 ov=## With ov (recommended)
-man-page=## As a man page (if compiled)
-manpage=## As a man page (if compiled)
+man-page=## As a man page
+manpage=## As a man page
 jump=## Jumping to a section
+html=## In the browser (HTML)
+browser=## In the browser (HTML)
+wiki=## As a wiki