feat(docs): generate Section 5 from function comment headers

The man-page-style comment header above each function in functions/*.fish
becomes the SSOT for that function's documentation. Writing a new function
and documenting it are now the same act.

- manualtools.parse_functions() parses every header carrying a # CATEGORY;
  absence of one is the opt-in, keeping bundled-plugin and prompt internals
  out of the manual with no exclusion list to maintain.
- build-manual.py generates entries for both --concat and --site, with
  **Dependencies:** rendered as links and a **Used by:** reverse index
  computed in one pass. Cross-category links are the navigation win.
- docs/manual/05-functions/*.md reduced to frontmatter-only stubs. Every
  intro measured zero words, so the category files were pure entry
  containers; ordering, titles, and helpKeywords routing are untouched.
- _first_sentence() unwraps the leading hard-wrapped paragraph and skips
  the whole Synopsis block, not just its label line. Site cards no longer
  truncate mid-clause or show a synopsis as their description.

Verification, per the design spec:
- test_concat_roundtrips_original scoped to sections 0-4 and 6-11. It
  guarded a format migration; this is a content migration.
- replaced by structural checks: one entry per categorised function, the
  required sections present, every category resolving to a stub with no
  stub empty, and every declared dependency resolving to a real function
  or a type -q-guarded binary.
- public functions lacking # CATEGORY warn rather than fail, so a new
  user-facing function going undocumented stays visible in CI.

24/24 checks pass. 94 entries generated from 94 parsed headers.

Also drops a stale claim from open-url's NOTES: config-help --html calls
xdg-open directly and has never called open-url.

docs/build-manual.py

@@ -18,6 +18,37 @@ import manualtools as mt
 
 DOCS = Path(__file__).parent
 MANUAL = DOCS / "manual"
+FUNCTIONS = DOCS.parent / "functions"
+SLUG_DIR = "reference"
+
+
+def _is_function_page(path: Path, root: Path) -> bool:
+    """True for a Section 5 category stub (not its index)."""
+    rel = path.relative_to(root)
+    return bool(rel.parts) and rel.parts[0].endswith("-functions") and rel.name != "index.md"
+
+
+def _entry_slug(title: str) -> str:
+    """The site's page slug for an entry heading."""
+    return re.sub(r"[^\w-]+", "-", title.strip().lower()).strip("-")
+
+
+def _entry_link(name: str, functions: dict) -> str:
+    """Link a dependency name to its entry page; plain code span if unknown."""
+    fn = functions.get(name)
+    if not fn:
+        return f"`{name}`"
+    category = re.sub(r"^\d+-", "", fn["CATEGORY"][0])
+    return f"[`{name}`](/{SLUG_DIR}/{category}/{_entry_slug(name)}/)"
+
+
+def _with_entries(body: str, path: Path, entries: dict) -> str:
+    """Append this category's generated `## name` entries to its stub body."""
+    generated = entries.get(path.stem, [])
+    if not generated:
+        return body
+    blocks = [f"## {name}\n\n{entry}" for name, entry in generated]
+    return "\n\n".join(([body] if body.strip() else []) + blocks)
 
 
 def build_concat(root: Path) -> str:
@@ -32,6 +63,7 @@ def build_concat(root: Path) -> str:
     present, its contents are re-emitted byte-for-byte as the leading
     `---`-fenced block, ahead of every heading.
     """
+    entries = build_entries(mt.parse_functions(FUNCTIONS))
     chunks: list[str] = []
     pandoc_path = root / "_pandoc.yml"
     if pandoc_path.exists():
@@ -43,6 +75,8 @@ def build_concat(root: Path) -> str:
             continue
         heading = fm.get("manTitle") or fm.get("title", path.stem)
         chunks.append("#" * (depth + 1) + " " + heading)
+        if _is_function_page(path, root):
+            body = _with_entries(body, path, entries)
         if body:
             chunks.append(mt.shift_headings(body, depth))
     return "\n\n".join(chunks) + "\n"
@@ -73,19 +107,46 @@ def _jsx_attr_escape(value: str) -> str:
 def _first_sentence(body: str) -> str:
     """Extract a one-line description from the start of an entry body.
 
-    `Synopsis:` lines are skipped: they restate the calling convention,
+    The `Synopsis:` block is skipped whole — label line plus its
+    deeper-indented continuation lines. It restates the calling convention,
     which the card already shows as its title, so using one as the card
     description wastes the line.
+
+    Source prose is hard-wrapped, so the leading paragraph is unwrapped
+    before the sentence match — otherwise a card truncates at the first
+    line break, mid-clause.
     """
-    for line in body.split("\n"):
+    para: list[str] = []
-        line = line.strip()
+    in_fence = False
-        if not line or line.startswith(("#", "```", "|", "-", "*", ">")):
+    syn_indent: int | None = None
+    for raw in body.split("\n"):
+        line = raw.strip()
+        indent = len(raw) - len(raw.lstrip())
+        if syn_indent is not None:
+            if line and indent <= syn_indent:
+                syn_indent = None
+            else:
+                continue
+        if line.startswith("```"):
+            in_fence = not in_fence
+            if para:
+                break
+            continue
+        if in_fence:
+            continue
+        if not line or line.startswith(("#", "|", "-", "*", ">")):
+            if para:
+                break
             continue
         if line.startswith("Synopsis:"):
+            syn_indent = indent
             continue
-        m = SENTENCE_RE.match(line)
+        para.append(line)
-        return (m.group(1) if m else line)[:160]
+    if not para:
         return ""
+    text = " ".join(para)
+    m = SENTENCE_RE.match(text)
+    return (m.group(1) if m else text)[:160]
 
 
 # Commands common enough in this manual that a block whose every line starts
@@ -222,8 +283,12 @@ def _prettify_block(block: list[str], entry_name: str | None) -> str:
 
     out: list[str] = []
     if lines and lines[0].startswith(SYNOPSIS_PREFIX):
-        synopsis = lines.pop(0)[len(SYNOPSIS_PREFIX) :].strip()
+        synopsis = [lines.pop(0)[len(SYNOPSIS_PREFIX) :].strip()]
-        out.append(f"```fish\n{synopsis}\n```")
+        # A multi-line synopsis is authored aligned under the first line;
+        # keep the whole thing in one fence rather than orphaning the rest.
+        while lines and lines[0].startswith(" "):
+            synopsis.append(lines.pop(0).strip())
+        out.append("```fish\n" + "\n".join(synopsis) + "\n```")
 
     para: list[str] = []
     for line in lines + [""]:
@@ -268,6 +333,76 @@ def prettify(body: str, entry_name: str | None = None) -> str:
     return "\n".join(out)
 
 
+ENTRY_HEADS = {"ARGUMENTS": "Arguments:", "RETURNS": "Returns:", "NOTES": "Notes:"}
+
+
+def render_entry(fn: dict[str, list[str]], used_by: list[str], link=None) -> str:
+    """Render one parsed function header as a manual entry body.
+
+    Emits the same man-page shape Section 5 was authored in — one 4-space
+    indented block opening with `Synopsis:` — so `prettify` keeps handling it
+    for the site and pandoc keeps handling it for the man page, with no
+    special case on either side.
+
+    `link` maps a function name to its markdown link, or is None for the man
+    page, where a URL in the middle of a sentence is noise.
+    """
+    out: list[str] = []
+    syn = fn.get("SYNOPSIS", [])
+    if syn:
+        pad = " " * len(SYNOPSIS_PREFIX + "  ")
+        out.append(f"{SYNOPSIS_PREFIX}  {syn[0]}")
+        out += [pad + line for line in syn[1:]]
+        out.append("")
+    for line in fn.get("DESCRIPTION", []):
+        out.append(line)
+    for label, head in ENTRY_HEADS.items():
+        body = fn.get(label)
+        if not body:
+            continue
+        out += ["", head] + ["  " + line for line in body]
+    if fn.get("EXAMPLE"):
+        out += [""] + fn["EXAMPLE"]
+
+    block = "\n".join((INDENT + line).rstrip() for line in out)
+
+    def names(raw: list[str]) -> list[str]:
+        return [n for n in re.split(r"[,\s]+", " ".join(raw)) if n]
+
+    refs = []
+    for label, values in (
+        ("Dependencies", names(fn.get("DEPENDENCIES", []))),
+        ("Used by", sorted(used_by)),
+    ):
+        if values:
+            rendered = ", ".join(link(v) if link else f"`{v}`" for v in values)
+            refs.append(f"**{label}:** {rendered}")
+    if refs:
+        block += "\n\n" + "\n\n".join(refs)
+    return block
+
+
+def build_entries(functions: dict[str, dict], link=None) -> dict[str, list[tuple[str, str]]]:
+    """Group rendered entries by category stem, ordered by function name.
+
+    The `Used by` reverse index is computed here in one pass rather than
+    authored: a bidirectional link maintained by hand drifts the moment one
+    side is edited.
+    """
+    used_by: dict[str, list[str]] = {}
+    for name, fn in functions.items():
+        for dep in re.split(r"[,\s]+", " ".join(fn.get("DEPENDENCIES", []))):
+            if dep in functions:
+                used_by.setdefault(dep, []).append(name)
+
+    out: dict[str, list[tuple[str, str]]] = {}
+    for name in sorted(functions):
+        fn = functions[name]
+        body = render_entry(fn, used_by.get(name, []), link)
+        out.setdefault(fn["CATEGORY"][0], []).append((name, body))
+    return out
+
+
 def _page_fm(fm: dict) -> dict:
     """Strip pipeline-only keys from frontmatter destined for the site."""
     return {k: v for k, v in fm.items() if k not in PIPELINE_KEYS}
@@ -315,6 +450,9 @@ def build_site(root: Path, out: Path) -> list[dict]:
         shutil.rmtree(out)
     out.mkdir(parents=True)
 
+    functions = mt.parse_functions(FUNCTIONS)
+    entries = build_entries(functions, link=lambda n: _entry_link(n, functions))
+
     sidebar: list[dict] = []
     functions_group: dict = {}
     for path, _depth in mt.walk(root):
@@ -341,7 +479,7 @@ def build_site(root: Path, out: Path) -> list[dict]:
         # upload. The pages build fine and never arrive — every entry 404s in
         # production while working locally. test_site_avoids_reserved_dir
         # guards this.
-        slug_dir = "reference"
+        slug_dir = SLUG_DIR
         if rel.name == "index.md":
             target = out / slug_dir / "index.md"
             target.parent.mkdir(parents=True, exist_ok=True)
@@ -360,12 +498,12 @@ def build_site(root: Path, out: Path) -> list[dict]:
         category = re.sub(r"^\d+-", "", rel.stem)
         cat_dir = out / slug_dir / category
         cat_dir.mkdir(parents=True, exist_ok=True)
-        intro, entries = _split_entries(body)
+        intro, page_entries = _split_entries(_with_entries(body, path, entries))
 
         cards = []
         links = []
-        for title, entry_body in entries:
+        for title, entry_body in page_entries:
-            entry_slug = re.sub(r"[^\w-]+", "-", title.strip().lower()).strip("-")
+            entry_slug = _entry_slug(title)
             desc = _first_sentence(entry_body)
             entry_fm = {"title": title}
             if desc:

docs/manual/05-functions/01-file-and-directory.md

@@ -7,158 +7,4 @@ helpKeywords:
 - files
 ---
 
-## cat
 
-    Synopsis:  cat [args...]
-    Wraps bat for files with syntax highlighting and line numbers.
-    Passes directories to ls. Falls back to /usr/bin/cat.
-
-    cat README.md
-    cat ~/projects/myapp
-
-## copy
-
-    Synopsis:  copy <source> <dest>
-    Wraps cp, stripping trailing slashes from source directories to
-    prevent unintended nesting inside the destination.
-
-    copy ./mydir/ ~/backup    # copies mydir INTO backup, not backup/mydir/
-
-## du
-
-    Synopsis:  du [--disk|--dir|--dua] [args...]
-    Smart disk-usage dispatcher:
-      --disk  force duf  (disk-level free/used overview)
-      --dir   force dust (per-directory tree breakdown)
-      --dua   force dua  (fast space analyzer)
-    Without flags, routes to the most appropriate tool by context.
-
-    du ~/Downloads
-    du --disk
-
-## dusize
-
-    Synopsis:  dusize [dir]
-    Human-readable disk usage for a directory via du -sh. Defaults to cwd.
-
-    dusize ~/Videos
-
-## lD
-
-    Synopsis:  lD [args...]
-    Lists directories only in long format with icons. Uses eza, falls back
-    to lsd, then system ls.
-
-    lD ~/projects
-
-## ls
-
-    Synopsis:  ls [args...]
-    Lists files in long format with icons and hyperlinks. Uses eza, falls
-    back to lsd, then system ls.
-
-    ls
-    ls -a ~/projects
-
-## lsr
-
-    Synopsis:  lsr [args...]
-    Lists files sorted by modification time, oldest first. Uses eza.
-
-## lss
-
-    Synopsis:  lss [args...]
-    Lists files sorted by size with gradient color scaling. Uses eza.
-
-## lstree
-
-    Synopsis:  lstree [args...]
-    Full recursive tree view with icons. Uses eza.
-
-    lstree ~/projects/myapp
-
-## lt
-
-    Synopsis:  lt [args...]
-    Tree view limited to depth 2 with icons. Uses eza.
-
-    lt ~/projects
-
-## ltr
-
-    Synopsis:  ltr [args...]
-    Lists files sorted by modification time, oldest first, long format with
-    age-based gradient scaling. Uses eza.
-
-## lx
-
-    Synopsis:  lx [args...]
-    Lists files sorted by extension, long format. Uses eza.
-
-## mkdir
-
-    Synopsis:  mkdir [args...]
-    Interactive mkdir that prints a tree of created directories.
-    Falls back to mkdir -p silently.
-
-    mkdir ~/projects/myapp/src
-
-## mkcd
-
-    Synopsis:  mkcd [-s] <dir>
-    Creates a directory (including parents) and cd into it. Prints a tree
-    of created dirs by default; -s/--silent suppresses output.
-
-    mkcd ~/projects/newapp/src
-
-## poke
-
-    Synopsis:  poke <file> [file...]
-    Creates files via touch, automatically creating any missing parent
-    directories first.
-
-    poke ~/projects/new/src/main.fish
-
-## rm
-
-    Synopsis:  rm [-e [opts] | -S | args...]
-    Safe rm wrapper routing to trash:
-
-      (no args)   List current trash contents
-      -e/--empty  Empty the trash (pass options to trash-empty)
-      -S/--secure Permanently delete via rm -rf + fstrim (irreversible)
-      -r/-R/--recursive  Move to trash
-      <paths>     Move to trash (safe delete)
-
-    Falls back to /usr/bin/rm when trash is unavailable.
-
-    rm file.txt           # moves to trash
-    rm -e                 # empty trash
-    rm -S sensitive.pem   # permanent delete
-
-## rg
-
-    Synopsis:  rg [args...]
-    In Kitty, wraps ripgrep with --hyperlink-format=kitty so search
-    results are clickable file links in the terminal. Falls back to
-    system rg in any other terminal. All other arguments pass through
-    unchanged.
-
-    rg "fish_greeting" ~/.config/fish/
-    rg -l "TODO" ~/projects/myapp
-
-## scrub
-
-    Synopsis:  scrub [-a] [-d] [-h]
-    Recursively removes OS metadata, editor artifacts, compiler output,
-    and dev caches using fd.
-
-      -a/--aggressive  Also removes node_modules, logs, .cache, IDE dirs,
-                       AI session artifacts
-      -d/--dry-run     Print what would be removed without deleting
-
-    scrub
-    scrub -a
-    scrub -d
-
----

docs/manual/05-functions/02-navigation.md

@@ -7,26 +7,4 @@ helpKeywords:
 - nav-fns
 ---
 
-## cdi
 
-    Synopsis:  cdi [query]
-    Interactive directory picker combining zoxide frecency with fzf.
-    Equivalent to zi.
-
-    cdi myproject
-
-## clone
-
-    Synopsis:  clone [args...]
-    Clone a git repository into a new Kitty window. Kitty-only.
-
-    clone https://github.com/user/repo.git
-
-## clonet
-
-    Synopsis:  clonet [args...]
-    Clone a git repository into a new Kitty tab. Kitty-only.
-
-    clonet https://github.com/user/repo.git
-
----

docs/manual/05-functions/03-editors-and-viewers.md

@@ -7,65 +7,4 @@ helpKeywords:
 - editors
 ---
 
-## edit
 
-    Synopsis:  edit [-V|-t] [-e EDITOR] [-c] [-x TEXT] [-n] [-v|-s] [FILE...]
-
-    Opens files in a text editor, choosing a terminal or GUI editor and
-    resolving a rich chain of fallbacks. With no --visual/--terminal flag the
-    mode is auto-detected: interactive terminals use the terminal editor
-    ($EDITOR), while detached invocations (e.g. desktop shortcuts) use the GUI
-    editor ($VISUAL). Clipboard contents and literal strings can be opened as
-    throwaway temp files. Editor output is suppressed unless --verbose.
-
-    GUI fallback chain:      zed → antigravity-ide → code → kate → kwrite →
-                             gnome-text-editor → gedit
-    Terminal fallback chain: nvim → vim → micro → nano → vi
-
-    Options:
-      -V, --visual      Force the GUI editor ($VISUAL or fallbacks)
-      -t, --terminal    Force the terminal editor ($EDITOR or fallbacks)
-      -e, --editor=X    Use a specific editor binary X
-      -c, --clipboard   Open the clipboard contents (as a temp file)
-      -x, --text=STR    Open STR as the contents of a new temp file
-      -n, --new         Force a new window/instance (best-effort)
-      -v, --verbose     Print the launch command and editor output
-      -s, --silent      Suppress all output, including the editor's
-      -h, --help        Show this help message
-
-    edit ~/.config/fish/config.fish
-    edit --visual notes.txt
-    edit --terminal --new todo.md
-    edit --editor=code --clipboard
-    edit --text="hello world"
-
-## fc
-
-    Synopsis:  fc [command_prefix]
-    Edit the last shell command (or one matching a prefix) in $EDITOR,
-    then execute the result. Bash-style fc behaviour.
-
-    fc
-    fc git
-
-## less
-
-    Synopsis:  less [args...]
-    Pager wrapper with fallback chain: $PAGER -> ov -> less -> more -> cat.
-
-    less /var/log/syslog
-
-## rawfish
-
-    Synopsis:  rawfish [args...]
-    Launches Fish with NO_TMUX=1, bypassing any tmux auto-attach logic.
-    Useful when you need a clean shell without session management.
-
-## view
-
-    Synopsis:  view [args...]
-    Opens files in nvim read-only mode (-R). Falls back to less.
-
-    view /etc/fstab
-
----

docs/manual/05-functions/04-git-and-version-control.md

@@ -7,84 +7,4 @@ helpKeywords:
 - git
 ---
 
-## auto-pull
 
-    Synopsis:  auto-pull [list]
-               auto-pull add [PATH]
-               auto-pull remove <NAME|PATH>
-               auto-pull status
-
-    Manages the registry of repositories that are background fast-forwarded
-    when you enter them (see "Auto-pull fast-forward" under the C2 component
-    reference). The fish-config repo is always covered as a baseline. The
-    registry is machine-local at `$__fish_user_dots_path/auto-pull.list` (defaults
-    to `~/.config/.user-dots/fish/auto-pull.list`), one absolute path per line,
-    and is never committed. Registry management works
-    even when C2 auto-execution is disabled; only the background sync is gated.
-
-      list               Show registered repos (default)
-      add [PATH]         Register PATH's git root (default: current repo)
-      remove <NAME|PATH> Unregister by basename or exact path
-      status             Show enabled/disabled state, repo count, list path
-
-    cd ~/src/qmk_firmware; and auto-pull add
-    auto-pull add ~/work/api
-    auto-pull list
-    auto-pull remove qmk_firmware
-
-## branch
-
-    Synopsis:  branch <branch_name>
-    Switches to a local branch, or creates it if it does not exist.
-
-    branch feature/new-ui
-
-## gi
-
-    Synopsis:  gi [-h] [-b] [-p] [-s] [-l] [targets...]
-    Generates .gitignore content from the gitignore.io API with MD5-based
-    deduplication (patterns already present are not re-appended).
-
-      -b/--boilerplate  Append generic boilerplate first
-      -p/--prompt       Prompt interactively for targets
-      -s/--stdout       Print to stdout instead of appending to .gitignore
-      -l/--list         List all available targets
-      targets           Comma-separated or space-separated target names
-
-    gi python,venv
-    gi -b -p
-    gi -s node > .gitignore
-
-## git-clean
-
-    Synopsis:  git-clean [-f]
-    Fetches and prunes the remote, fast-forwards the current branch, then
-    deletes local branches whose remote tracking branch has been deleted.
-    Switches to main/master automatically if the current branch is orphaned.
-
-      -f/--force  Force-delete unmerged branches too
-
-    git-clean
-    git-clean --force
-
-## gitup
-
-    Synopsis:  gitup [args...]
-    Fetches updates from the remote and shows git status. Extra args are
-    forwarded to git fetch.
-
-    gitup
-    gitup --all
-
-## gitui
-
-    Synopsis:  gitui [args...]
-    Launches gitui with the Catppuccin Frappe theme pre-applied.
-
-## hist
-
-    Synopsis:  hist
-    Searches shell history with fzf, inserts the selection into the command
-    line, and copies it to the clipboard via wl-copy.
-
----

docs/manual/05-functions/05-package-management.md

@@ -8,53 +8,4 @@ helpKeywords:
 - packages
 ---
 
-## pkg
 
-    Synopsis:  pkg [-h] [-i|-u] <package> [package...]
-    Installs or removes packages using the detected system package manager.
-    Supports: paru, yay, pacman, apt, dnf, zypper, yum, brew, pkg.
-
-      (no flag)    Auto mode: installs missing packages, removes installed ones
-      -i/--install  Force install
-      -u/--uninstall  Force uninstall
-
-    pkg firefox             # auto: install if missing, remove if present
-    pkg -i ripgrep fd       # force install
-    pkg -u cowsay           # force uninstall
-
-    The package-installed check uses the correct query for each PM:
-      pacman/paru/yay  pacman -Qi
-      apt              dpkg -s
-      dnf/zypper/yum   rpm -q
-      brew             brew list
-      pkg              pkg info
-
-## search
-
-    Synopsis:  search [args...]
-    Interactive AUR package search and install via paru or yay.
-    Arch Linux only.
-
-    search neovim
-
-## upgrade
-
-    Synopsis:  upgrade
-    Full system upgrade via paru -Syu --noconfirm or yay -Syu --noconfirm.
-    Arch Linux only.
-
-## cleanup
-
-    Synopsis:  cleanup
-    Lists and removes orphan packages via pacman, logging their names to
-    ~/.removed_orphans. Arch Linux only.
-
-## parur
-
-    Synopsis:  parur
-    Opens an fzf picker of all installed packages (with pacman -Qi previews),
-    then removes the selected packages via paru or yay. Arch Linux only.
-
-    parur
-
----

docs/manual/05-functions/06-dependency-management.md

@@ -7,41 +7,4 @@ helpKeywords:
 - deps
 ---
 
-## fish-deps
 
-    Synopsis:  fish-deps [status|install|update|sync]
-    Unified command for managing all tools this configuration depends on.
-
-      status   (default) Show installed/missing status grouped by tier
-      install  Interactively install each missing dependency
-      update   Update all installed dependencies
-      sync     Install missing deps, then update all
-
-    Install method priority (highest to lowest):
-      1. git+cargo source build (fish shell itself)
-      2. cargo (Rust tools — gets latest crate version)
-      3. system PM (paru/apt/brew/etc.)
-      4. git clone (fzf)
-      5. curl installer (starship, fisher, uv)
-
-    When multiple methods are available you are prompted to choose.
-
-    Dependencies are grouped into three tiers:
-
-      Required      fish, fzf, zoxide
-      Integrations  wakatime, tailscale
-      Recommended   cargo, starship, uv, direnv, paru, yay, eza, lsd, bat,
-                    btop, dust, duf, prettyping, ov, ripgrep, lazygit,
-                    lazydocker, trash, kitty, wezterm, python3, yt-dlp
-
-    fish-deps
-    fish-deps install
-    fish-deps update
-    fish-deps sync
-
-## check_fish_deps
-
-    Synopsis:  check_fish_deps
-    Backwards-compatibility alias for `fish-deps status`.
-
----

docs/manual/05-functions/07-system-and-monitoring.md

@@ -7,57 +7,4 @@ helpKeywords:
 - system
 ---
 
-## top
 
-    Synopsis:  top [args...]
-    Launches btop as a modern resource monitor. Falls back to system top.
-
-## swapstat
-
-    Synopsis:  swapstat
-    Displays a colorized memory report: kernel swappiness, zRAM compression
-    ratio, zRAM device details, and active swap priorities.
-
-## sbver
-
-    Synopsis:  sbver [--brief]
-    Verifies Secure Boot signatures on all EFI binaries tracked by sbctl.
-    Color-codes results: green checkmark (verified), red X (unsigned).
-    Prints a pass/fail summary.
-
-      --brief  Suppress per-file output, show only the summary
-
-    sbver
-    sbver --brief
-
-## ports
-
-    Synopsis:  ports
-    Lists active TCP listeners with lsof, showing port/address without
-    hostname resolution.
-
-## screensleep
-
-    Synopsis:  screensleep
-    Turns off the display via KDE PowerDevil's "Turn Off Screen" action,
-    invoked through busctl.
-
-## lock
-
-    Synopsis:  lock
-    Locks the current desktop session using loginctl lock-session.
-
-## sudo-toggle
-
-    Synopsis:  sudo-toggle
-    Toggles the sudo NOPASSWD rule on/off via /etc/sudoers.d/nofail-toggle.
-    Useful for automated tasks that would otherwise require password entry.
-
-## limine-edit
-
-    Synopsis:  limine-edit
-    Opens /boot/limine.conf in sudoedit, then automatically re-enrolls the
-    config hash, runs CachyOS boot hooks, and re-signs Secure Boot files.
-    Combines the edit and sign steps into a single command.
-
----

docs/manual/05-functions/08-terminal-management.md

@@ -7,54 +7,4 @@ helpKeywords:
 - terminal-mgmt
 ---
 
-## tab
 
-    Synopsis:  tab [args...]
-    Opens a new tab in Kitty (kitty @ launch --type=tab), WezTerm
-    (wezterm cli spawn), or Konsole. Uses current working directory,
-    or $cdto if set.
-
-    tab
-
-## split
-
-    Synopsis:  split [-h|-v] [command...]
-    Opens a new pane in Kitty or WezTerm, optionally running a command.
-
-      -h/--horizontal  (default) Split below
-      -v/--vertical    Split to the right
-
-    split
-    split -v nvim README.md
-
-## spwin
-
-    Synopsis:  spwin [args...]
-    Spawns a new terminal OS window in Kitty (via spawn-window.sh or
-    kitty @ launch --type=os-window) or WezTerm (wezterm cli spawn --new-window).
-
-## detach
-
-    Synopsis:  detach [-h] [--version] <command> [args...]
-    Runs a command fully detached via nohup with stdout/stderr discarded.
-    The command survives the current session.
-
-    detach rsync -a ./data remote:/backup/
-
-## bkg
-
-    Synopsis:  bkg <command> [args...]
-    Launches a command in the background via nohup with output discarded.
-    Simpler than detach; no version flag.
-
-    bkg firefox
-
-## ssh
-
-    Synopsis:  ssh [args...]
-    In Kitty, wraps ssh with kitten ssh for better terminal integration
-    (multiplexing, copy/paste support). Falls back to system ssh elsewhere.
-
-    ssh user@host
-
----

docs/manual/05-functions/09-clipboard.md

@@ -7,26 +7,4 @@ helpKeywords:
 - clipboard
 ---
 
-## y
 
-    Synopsis:  y [text...]
-    Copies text to the clipboard via wl-copy (Wayland) or xclip (X11).
-    Reads from stdin if no arguments given.
-
-    y "hello world"
-    ls | y
-    cat file.txt | y
-
-## p
-
-    Synopsis:  p [args...]
-    Outputs clipboard contents to stdout.
-
-    p | grep foo
-    p > file.txt
-
-## paste
-
-    Alias for p. Identical behaviour.
-
----

docs/manual/05-functions/10-network.md

@@ -7,38 +7,4 @@ helpKeywords:
 - network
 ---
 
-## gip
 
-    Synopsis:  gip
-    Fetches and prints both the public IPv4 and IPv6 address via
-    icanhazip.com.
-
-## gip4
-
-    Synopsis:  gip4
-    Fetches and prints the public IPv4 address.
-
-## gip6
-
-    Synopsis:  gip6
-    Fetches and prints the public IPv6 address. Returns 1 if IPv6 is
-    unavailable.
-
-## ping
-
-    Synopsis:  ping [args...]
-    Wraps prettyping with --nolegend. Pass --legend to show the legend.
-    Falls back to system ping.
-
-    ping google.com
-
-## qr
-
-    Synopsis:  qr [text...]
-    Generates a UTF-8 QR code from text or stdin. Uses qrencode locally;
-    falls back to the qrenco.de API.
-
-    qr "https://example.com"
-    echo "https://example.com" | qr
-
----

docs/manual/05-functions/11-pager-and-logging.md

@@ -7,41 +7,4 @@ helpKeywords:
 - logging
 ---
 
-## logs
 
-    Synopsis:  logs [-c <category>]
-    Interactively browses terminal log files sorted newest-first using fzf.
-
-      -c/--category  Filter to: scrollback, paru, or yay
-
-    Keybindings inside the fzf browser:
-      Enter    Open in $PAGER
-      Ctrl+E   Open in $EDITOR
-      Ctrl+D   Delete (with confirmation)
-      ?        Toggle keybind help overlay
-
-    Paru and yay logs open in ov with syntax highlighting and sticky section
-    headers. Scrollback logs open in ov with per-command sticky prompt headers
-    based on OSC 133 markers.
-
-    logs
-    logs -c paru
-    logs -c scrollback
-
-## smart_exit
-
-    Synopsis:  smart_exit [-n]
-    Closes the shell session. In Kitty, captures the terminal scrollback to
-    a timestamped log file in $SCROLLBACK_HISTORY_DIR before exiting.
-    Automatically prunes the oldest logs when the count exceeds
-    $SCROLLBACK_HISTORY_MAX_FILES.
-
-      -n/--no-log  Exit without saving a scrollback log
-
-    The exit builtin is wired to smart_exit for interactive sessions.
-    Typing exit or Ctrl+D behaves identically to smart_exit.
-
-    smart_exit
-    smart_exit --no-log
-
----

docs/manual/05-functions/12-ai-and-developer-tools.md

@@ -7,110 +7,4 @@ helpKeywords:
 - ai
 ---
 
-## agy
 
-    Synopsis:  agy [args...]
-    Wrapper for the agy Antigravity AI CLI. Before launching, delegates to
-    agents-init --agents to ensure AGENTS/ is scaffolded and CLAUDE.md is
-    symlinked to AGENTS/AGENTS.md in the current project, then forwards all
-    arguments verbatim to the real agy binary. Command shadow (C1): when
-    __fish_config_op_aliases (or the master) is disabled, the call is
-    passed through to the real agy binary unchanged.
-
-    agy chat
-    agy resume
-
-## antigravity-ide
-
-    Synopsis:  antigravity-ide [args...]
-    Runs the antigravity-ide editor with warnings filtered.
-
-## agents-init
-
-    Synopsis:  agents-init [--agents | --plugins]
-    Scaffold an AGENTS/ sub-repository for tracking agent specs, plans, specs,
-    and dev logs. Creates AGENTS/ as a standalone git repo, moves any existing
-    AGENTS.md into it, and replaces it with a relative symlink (plus
-    CLAUDE.md -> AGENTS/AGENTS.md so Claude Code picks up the shared agent
-    instructions). Consolidates plans/ and specs/ directly under AGENTS/
-    (merging any legacy docs/plans, docs/superpowers/plans, or old
-    AGENTS/plugins/ locations into the canonical AGENTS/<tgt>), creates
-    AGENTS/devlogs/, and wires docs/superpowers/{plans,specs} symlinks back to
-    them. Adds managed paths to .gitignore and auto-commits every change inside
-    the AGENTS/ sub-repo; pulls first when the sub-repo has an upstream.
-    Fully idempotent: a second run produces no output and no new commits.
-    Flags: --agents re-runs only the AGENTS.md / symlink step; --plugins
-    re-runs only the plans/specs/devlogs wiring step. Called automatically by
-    the claude and agy wrappers on every invocation.
-
-    Structure versioning: each AGENTS/ repo carries a self-contained version
-    bumper. AGENTS/.version holds MAJOR.MINOR.PATCH (seeded 1.0.0). Committed
-    git hooks under AGENTS/.agents-tools/ (wired via core.hooksPath) bump it on
-    every commit: MINOR (resetting PATCH) when the tracked directory set
-    changes, PATCH otherwise; MAJOR is manual-only. A prepare-commit-msg hook
-    appends "(vX.Y.Z)" to the commit subject. Downstream tooling can read
-    AGENTS/.version - a changed MINOR field signals a structure change. Because
-    core.hooksPath is a single setting, the local override would otherwise
-    shadow your global hooks; after bumping the version, each shim chains
-    (execs) to the global/system core.hooksPath hook of the same name so global
-    pre-commit / prepare-commit-msg hooks (e.g. ggshield, Git LFS) still run.
-    The script and hooks are shipped from scripts/agents-tools/ and refreshed
-    when their version marker is stale.
-
-    agents-init
-    agents-init --agents
-    agents-init --plugins
-
-## claude
-
-    Synopsis:  claude [args...]
-    Wrapper for the claude CLI. Before launching, delegates to agents-init
-    --agents to ensure AGENTS/ is scaffolded and CLAUDE.md is symlinked to
-    AGENTS/AGENTS.md in the current project, then forwards all arguments
-    verbatim to the real claude binary. Command shadow (C1): when
-    __fish_config_op_aliases (or the master) is disabled, the call is
-    passed through to the real claude binary unchanged.
-
-    claude
-    claude --resume
-
-## claude-docs
-
-    Synopsis:  claude-docs
-    Invokes Claude Code to analyze recent repository changes and update
-    README.md, ensuring all documented features and examples are accurate.
-
-## claude-pr
-
-    Synopsis:  claude-pr
-    Invokes Claude Code to run the full PR workflow: create branch,
-    conventional commit, verification, push, and open a PR with a manual
-    verification checklist.
-
-## qc
-
-    Synopsis:  qc [prompt...]
-    Quick-chat wrapper around the aichat LLM CLI that defaults to the "cli"
-    role - a system prompt tuned for concise, terminal-friendly output. On
-    first use it installs the bundled role by symlinking
-    scripts/cli-agent.md to $XDG_CONFIG_HOME/aichat/roles/cli.md (creating
-    the directory if needed). Inherits every aichat flag and tab completion
-    (--wraps aichat); passing --role/-r overrides the default role, so qc
-    forwards to aichat unchanged. The function is only defined when aichat
-    is installed. Run qc --help for aichat's full flag reference with the
-    command name rewritten to qc.
-
-    qc "how do I list open ports on linux?"
-    qc -m ollama:llama3 "explain this error"
-    qc --role coder "refactor this function"
-
-## superpowers
-
-    Synopsis:  superpowers [on|off] [-g]
-    Enables or disables the Superpowers plugin for Antigravity and Claude
-    Code at workspace/project scope (default) or user scope (-g/--global).
-
-    superpowers on
-    superpowers off -g
-
----

docs/manual/05-functions/13-media-and-utilities.md

@@ -7,48 +7,4 @@ helpKeywords:
 - media
 ---
 
-## dng2avif
 
-    Synopsis:  dng2avif [-i <file>] [-o <file>] [-q <n>] [-s <n>] [input.dng]
-    Converts a DNG raw image to a 10-bit HDR AVIF using an ImageMagick,
-    ffmpeg, avifenc pipeline with metadata sync via exiftool.
-
-      -i/--input    Input file (or positional arg)
-      -o/--output   Output file (default: same name, .avif extension)
-      -q/--quality  Quality 0-100 (default 92)
-      -s/--speed    Encoding speed 0-10 (default 3)
-
-    dng2avif photo.dng
-    dng2avif -q 85 -s 5 -i shot.dng -o out.avif
-
-## steam-dl
-
-    Synopsis:  steam-dl
-    Launches Steam under systemd-inhibit, preventing the system from going
-    idle or sleeping while a download is in progress.
-
-## spark
-
-    Synopsis:  spark [--min=<n>] [--max=<n>] [numbers...]
-    Renders a Unicode sparkline bar chart for a sequence of numbers.
-    Reads from stdin if no numbers are given.
-
-    spark 1 1 2 5 14 42
-    echo "3 7 2 9 1" | spark
-
-## yt-dlp
-
-    Synopsis:  yt-dlp [args...] URL [URL...]
-    Wraps yt-dlp, prepending sane defaults: --sponsorblock-remove all,
-    --embed-subs, --embed-metadata, and --embed-thumbnail. Each default
-    is suppressed when you already pass that flag, its alias, or its
-    negation (e.g. --no-embed-thumbnail drops the thumbnail default;
-    --no-sponsorblock or your own --sponsorblock-remove drops ours). All
-    other arguments pass through unchanged, and --help falls through to
-    real yt-dlp. Opinionated component (C1 aliases); when disabled it
-    passes straight through to the system yt-dlp.
-
-    yt-dlp dQw4w9WgXcQ
-    yt-dlp --no-embed-thumbnail dQw4w9WgXcQ
-
----

docs/manual/05-functions/14-miscellaneous.md

@@ -7,279 +7,4 @@ helpKeywords:
 - miscfns
 ---
 
-## config-help
 
-    Synopsis:  config-help [SECTION]
-               config-help --html
-               config-help [SECTION] --man
-               config-help -h | --help
-
-    Opens the offline fish shell configuration manual. Without flags, opens
-    the Markdown source in the best available pager (ov > bat > man > less >
-    cat). If SECTION is given, jumps to the first heading matching that
-    keyword (case-insensitive; checks fish-config.index aliases first).
-
-    Flags:
-      --html / -w   Open the published documentation website
-                    (https://fish-config-docs.pages.dev/) in the default
-                    browser via xdg-open. Deep links to a section aren't
-                    supported; if SECTION is given, a note points you to the
-                    site's search box instead.
-      --man  / -m   Open docs/fish-config.1 via man -l directly.
-                    If SECTION is given, jumps to the nearest match.
-      --help / -h   Print usage and navigation key reference.
-
-    config-help keybindings
-    config-help pkg
-    config-help --html
-    config-help --man
-    config-help pkg --man
-
-    Also available as: help config [SECTION] [FLAGS]
-
-## open-url
-
-    Synopsis:  open-url [-s|--silent] [-v|--verbose] <url>
-               open-url -h | --help
-
-    Opens a URL or file:// URI in the best available graphical web browser,
-    backgrounded so it never blocks the terminal. Resolves a real browser
-    binary rather than deferring to xdg-open, whose MIME dispatch can hand
-    local text/html files to non-browser apps (e.g. ebook readers).
-
-    Silent by default: prints nothing on success (errors always go to
-    stderr). Pass --verbose / -v to report which browser is launched;
-    --silent / -s is accepted for explicitness.
-
-    Resolution order:
-      1. $fish_help_browser  (explicit override)
-      2. $BROWSER            (validated; errors if not a command)
-      3. xdg-mime default handler for x-scheme-handler/https
-      4. First known browser binary found in a built-in list
-      5. xdg-open            (last resort)
-
-    open-url https://git.rootiest.dev/rootiest/fish-config
-    open-url -v https://fish-config-docs.pages.dev/
-
-    Used internally by config-help --html.
-
-    Typo abbreviation: url-open (expands to open-url on space/enter).
-
-## repo-open
-
-    Synopsis:  repo-open [-p|--print] [-r|--root]
-               repo-open -h | --help
-
-    Opens the web page for the current repository's `origin` remote in a
-    browser (via open-url). Deep-links to the current branch when it exists
-    on the remote — falling back to the remote's default branch (main/master)
-    otherwise — and to the current sub-directory when run below the repo root.
-
-    The remote URL is normalized from HTTPS and SSH/scp forms
-    (git@host:owner/repo.git, ssh://…, https://…). The web path layout is
-    provider-specific; the provider is resolved in order:
-
-      1. git config browse.provider   (per-repo or --global override)
-      2. Hostname heuristic           (github / gitlab / gitea / bitbucket;
-                                        codeberg → gitea)
-      3. Default: github-style layout
-
-    Self-hosted hosts the heuristic can't classify (a Gitea/GitLab instance
-    on a custom domain) need a one-time override:
-
-      git config browse.provider gitea
-
-    Flags:
-      --print / -p   Print the resolved URL instead of opening it.
-      --root  / -r   Ignore the current sub-directory; link to the repo root.
-      --help  / -h   Show usage.
-
-    repo-open
-    repo-open --print
-    repo-open --root
-
-    Typo abbreviation: open-repo (expands to repo-open on space/enter).
-
-## config-update
-
-    Synopsis:  config-update [-h] [-n] [-f]
-
-    Pulls the latest fish configuration from the upstream repository
-    (https://git.rootiest.dev/rootiest/fish-config.git) into ~/.config/fish.
-    The remote URL is hard-coded, so this works on fresh clones with no git
-    remote configured. All git output is suppressed; colored messages report
-    fetch and merge status. After a successful pull, run `exec fish` to
-    reload.
-
-    Flags:
-      --dry-run / -n   Fetch and show available commits without applying them.
-      --force  / -f    Stash local changes, pull, then restore the stash.
-      --help   / -h    Show usage.
-
-    config-update
-    config-update --dry-run
-    config-update --force
-
-## config-settings
-
-    Synopsis:  config-settings [-h]
-
-    Opens an interactive TUI for managing fish configuration settings across
-    four pages, without having to type or remember variable names. Tab cycles
-    forward through the pages; Shift-Tab cycles backward.
-
-      Universal — opinionated category toggles (C1–C6) + master, persistent (set -U)
-      Session   — the same toggles, current shell only (set -g)
-      Sponge    — sponge history-scrubbing settings: delay, successful exit
-                  codes, purge-only-on-exit, allow-previously-successful, and
-                  extra sensitive variable-name tokens
-      Paths     — scrollback log directory, scrollback max files, the
-                  user-dots path, and the user-dots convenience symlink toggle
-                  (Dots link)
-
-    Toggle rows use ← → (or h/l) along an OFF ← DEFAULT → ON scale; DEFAULT
-    erases the variable so the master switch / built-in default applies. Value
-    rows (the path/int/list settings on the Sponge and Paths pages) use Enter to
-    edit inline; ← / h clears the value back to its default. List rows (e.g.
-    Extra secret, OK codes) accept values separated by commas and/or whitespace
-    — "A, B", "A,B" and "A B" all yield the same two entries. Changes apply
-    immediately. Always available regardless of the __fish_config_opinionated
-    master state.
-
-    The Sponge and Paths pages always write universal variables — these are
-    persistent, set-and-forget settings with no per-session scope. Editing a
-    scrollback row updates both the __fish_scrollback_history_* source-of-truth
-    variables and the exported SCROLLBACK_HISTORY_* mirrors, so the AUR/tmux/
-    zellij log wrappers (which read the exported names) see the change in the
-    running session.
-
-    The panel adapts to the terminal width automatically, selecting from
-    four layout tiers (with a 6-column buffer on each side before stepping
-    up to the next tier) and horizontally centering the box. The panel
-    redraws within ~0.3 s of a terminal resize with no keypress required.
-
-      COLUMNS >= 90  →  78-wide panel (most detail)
-      COLUMNS >= 86  →  74-wide panel
-      COLUMNS >= 82  →  70-wide panel
-      COLUMNS  < 82  →  52-wide panel (default)
-
-    Navigation:
-      ↑ ↓ / k j     Move cursor
-      ← → / h l     Toggle rows: OFF ← DEFAULT → ON
-      ←  / h        Value rows: clear to default
-      Enter         Value rows: edit inline (Sponge / Paths pages)
-      Tab / S-Tab   Next / previous page
-      q / Escape    Exit
-
-    Flags:
-      --help / -h   Show usage.
-
-    config-settings
-
-## config-toggle (deprecated)
-
-    Deprecated alias for config-settings. Prints a deprecation notice to
-    stderr, then delegates all arguments to config-settings.
-
-    config-toggle
-
-## bash
-
-    Synopsis:  bash [args...]
-    Switches to bash, with XDG config applied. On exit, $SHELL is reset
-    back to fish.
-
-## bd-pull
-
-    Synopsis:  bd-pull <owner/repo>
-    Fetches unlinked Gitea issues and creates local Beads entries, updating
-    issue titles with the assigned Beads IDs.
-    Requires $GITEA_TOKEN and $GITEA_URL to be set.
-
-    bd-pull rootiest/fish-config
-
-## cheat
-
-    Synopsis:  cheat <topic> [args...]
-    Displays a colorized cheatsheet using cheat -c, falls back to tldr,
-    then man.
-
-    cheat tar
-    cheat git
-
-## cffetch / ffetch
-
-    Synopsis:  cffetch [args...]  /  ffetch [args...]
-    Clears the screen and displays system information via fastfetch with
-    the custom config at ~/.fastfetch.jsonc. Falls back to neofetch.
-
-## dockup
-
-    Synopsis:  dockup [-h] [directory]
-    Pulls latest Docker images, restarts services in the given Docker
-    Compose project, and prunes dangling images.
-
-    dockup ~/myapp
-
-## joplin
-
-    Synopsis:  joplin [args...]
-    Runs the Joplin CLI with Node.js deprecation warnings suppressed.
-
-    joplin ls
-
-## ld
-
-    Synopsis:  ld
-    Launches lazydocker targeting the currently active Docker context,
-    detected via docker context inspect.
-
-## replay
-
-    Synopsis:  replay <commands>
-    Runs Bash commands and replays any resulting changes to environment
-    variables, aliases, and the working directory back into the current
-    Fish session. Useful for sourcing Bash scripts.
-
-    replay "source ~/.bashrc"
-    replay "export FOO=bar"
-
-## kitty-logging
-
-    Synopsis:  kitty-logging [install|uninstall|status|dismiss] [-h]
-
-    Manages the Kitty scrollback watcher that powers C5 logging. Ships a
-    canonical watcher and symlinks it into the Kitty config directory (so it
-    always tracks the source), wiring it into kitty.conf through a
-    sentinel-marked managed block. Commenting out any conflicting watcher line
-    avoids double-capture.
-
-    Commands:
-      install    Symlink the watcher and add the managed block
-      uninstall  Remove the managed block and the watcher symlink
-      status     Show wiring, installed watcher version, and C5 state
-      dismiss    Stop the per-session setup reminder
-
-    Runtime capture stays governed by the C5 .logging_disabled sentinel, so
-    disabling __fish_config_op_logging makes the watcher inert without
-    uninstalling. Install affects new Kitty windows only.
-
-    Example:
-      kitty-logging install
-      kitty-logging status
-
-## tmux-clean
-
-    Synopsis:  tmux-clean
-    Kills all detached (unattached) tmux sessions, leaving attached ones
-    running.
-
-## wake-lock
-
-    Synopsis:  wake-lock <command> [args...]
-    Runs a command under systemd-inhibit, preventing the system from going
-    idle or sleeping until the command completes.
-
-    wake-lock rsync -avz src/ dest/
-
----

docs/manualtools.py

@@ -3,7 +3,8 @@
 # SPDX-License-Identifier: AGPL-3.0-or-later
 """Shared helpers for the docs/manual SSOT pipeline.
 
-Frontmatter parsing, deterministic tree ordering, and heading level shifts.
+Frontmatter parsing, deterministic tree ordering, heading level shifts, and
+the `functions/*.fish` comment-header parser that is the SSOT for Section 5.
 Used by build-manual.py and verify-manual.py.
 """
 
@@ -57,6 +58,88 @@ def shift_headings(body: str, by: int) -> str:
     return "\n".join(out)
 
 
+HEADER_LABEL = re.compile(r"^#\s+([A-Z][A-Z ]*[A-Z])\s*$")
+FUNC_DEF = re.compile(r"^\s*function\s+(\S+)")
+SECTIONS = (
+    "CATEGORY",
+    "DEPENDENCIES",
+    "SYNOPSIS",
+    "DESCRIPTION",
+    "ARGUMENTS",
+    "RETURNS",
+    "EXAMPLE",
+    "NOTES",
+)
+
+
+def _header_blocks(lines: list[str]) -> list[tuple[int, dict[str, list[str]]]]:
+    """Find every man-page comment header in a file's lines.
+
+    Yields (index of the line that ended the block, {LABEL: body lines}).
+    Body lines keep any indentation deeper than the standard `#   ` prefix,
+    which is what lets nested option tables survive into the rendered entry.
+    Comment runs carrying no `# LABEL` line at all (the copyright preamble,
+    ordinary inline comments) produce nothing.
+    """
+    out: list[tuple[int, dict[str, list[str]]]] = []
+    cur: dict[str, list[str]] = {}
+    label: str | None = None
+    for i, line in enumerate(lines + [""]):
+        if not line.startswith("#"):
+            if cur:
+                out.append((i, cur))
+            cur, label = {}, None
+            continue
+        m = HEADER_LABEL.match(line)
+        if m:
+            label = m.group(1)
+            cur.setdefault(label, [])
+        elif label is not None:
+            body = line[1:]
+            cur[label].append(body[3:] if body.startswith("   ") else body.strip())
+    return out
+
+
+def _trailing_blanks(lines: list[str]) -> int:
+    """Count the blank `#` separator lines closing a section."""
+    n = 0
+    while n < len(lines) and not lines[len(lines) - 1 - n].strip():
+        n += 1
+    return n
+
+
+def parse_functions(root: Path) -> dict[str, dict[str, list[str]]]:
+    """Parse the comment header above every documented public function.
+
+    `root` is the repository's `functions/` directory. Returns
+    `{name: {LABEL: [lines]}}`.
+
+    `# CATEGORY` is the opt-in: a header without one produces no entry. That
+    keeps bundled-plugin and prompt internals (`fish_prompt`, `sponge_filter_*`,
+    `fisher`, …) out of the manual with no exclusion list to maintain.
+
+    A file carrying exactly one header is associated with its own stem, so a
+    `function` nested inside a `type -q` guard still resolves. Only files with
+    several headers walk forward to the next `function` definition.
+    """
+    out: dict[str, dict[str, list[str]]] = {}
+    for path in sorted(root.glob("*.fish")):
+        lines = path.read_text(encoding="utf-8").split("\n")
+        blocks = _header_blocks(lines)
+        for end, sections in blocks:
+            if len(blocks) == 1:
+                name = path.stem
+            else:
+                after = (m.group(1) for ln in lines[end:] if (m := FUNC_DEF.match(ln)))
+                name = next(after, path.stem)
+            if name.startswith("_") or "CATEGORY" not in sections:
+                continue
+            out[name] = {
+                k: v[: len(v) - _trailing_blanks(v)] for k, v in sections.items()
+            }
+    return out
+
+
 def _sort_key(entry: Path) -> tuple:
     """Order by sidebar.order when present, else by filename. Stable."""
     target = entry / "index.md" if entry.is_dir() else entry

docs/verify-manual.py

@@ -4,6 +4,7 @@
 """Verification checks for the docs/manual SSOT pipeline."""
 
 import importlib.util
+import re
 import sys
 import tempfile
 from pathlib import Path
@@ -109,14 +110,113 @@ def test_manual_tree_exists():
     assert len(cats) == 14, f"expected 14 function categories, got {len(cats)}: {cats}"
 
 
-def test_function_entries_promoted_to_h2():
+def test_function_stubs_carry_no_entries():
+    """Category files are stubs: entries come from functions/*.fish headers.
+
+    An authored `##` entry here would be a second copy of a function's
+    documentation — exactly the duplication the header-SSOT migration
+    removed — and the generator would emit its own entry alongside it.
+    """
     root = Path(__file__).parent / "manual" / "05-functions"
     for path in root.glob("*.md"):
         if path.name == "index.md":
             continue
         _, body = mt.parse(path)
-        assert "\n### " not in f"\n{body}", f"{path.name} still has H3 entries"
+        stray = [ln for ln in body.split("\n") if ln.startswith(("## ", "### "))]
-        assert "\n## " in f"\n{body}", f"{path.name} has no H2 function entries"
+        assert not stray, f"{path.name} has authored entries: {stray}"
+
+
+def _parsed_functions() -> dict[str, dict[str, list[str]]]:
+    return mt.parse_functions(Path(__file__).parent.parent / "functions")
+
+
+def test_every_categorised_function_produces_one_entry():
+    import build_manual
+
+    functions = _parsed_functions()
+    entries = build_manual.build_entries(functions)
+    got = [name for names in entries.values() for name, _ in names]
+    assert sorted(got) == sorted(functions), (
+        f"entry/function mismatch: "
+        f"{sorted(set(functions) ^ set(got))}"
+    )
+    assert len(got) == len(set(got)), "a function produced more than one entry"
+
+
+def test_entries_carry_the_required_sections():
+    missing = []
+    for name, fn in _parsed_functions().items():
+        absent = [s for s in ("SYNOPSIS", "DESCRIPTION", "EXAMPLE") if not fn.get(s)]
+        if absent:
+            missing.append(f"{name}: {', '.join(absent)}")
+    assert not missing, "headers missing required sections:\n  " + "\n  ".join(missing)
+
+
+def test_every_category_resolves_to_a_stub():
+    root = Path(__file__).parent / "manual" / "05-functions"
+    stubs = {p.stem for p in root.glob("*.md") if p.name != "index.md"}
+    used = {}
+    for name, fn in _parsed_functions().items():
+        used.setdefault(" ".join(fn.get("CATEGORY", [])).strip(), []).append(name)
+    unknown = {c: v for c, v in used.items() if c not in stubs}
+    assert not unknown, f"# CATEGORY values with no stub: {unknown}"
+    empty = sorted(stubs - set(used))
+    assert not empty, f"category stubs generating zero entries: {empty}"
+
+
+def test_dependencies_resolve():
+    """Every declared # DEPENDENCIES name must be a real function or binary.
+
+    Catches typos, and catches stale entries when a dependency is renamed
+    or deleted. External binaries are accepted when some file in the tree
+    guards them with `type -q`, which is this repo's convention.
+    """
+    repo = Path(__file__).parent.parent
+    functions = _parsed_functions()
+    known = {p.stem for p in (repo / "functions").glob("*.fish")} | set(functions)
+    for path in list(repo.glob("conf.d/*.fish")) + list((repo / "functions").glob("*.fish")):
+        known |= set(re.findall(r"type -q\s+(\S+)", path.read_text(encoding="utf-8")))
+    dangling = []
+    for name, fn in functions.items():
+        for dep in (d for d in re.split(r"[,\s]+", " ".join(fn.get("DEPENDENCIES", []))) if d):
+            if dep not in known:
+                dangling.append(f"{name} -> {dep}")
+    assert not dangling, "unresolvable # DEPENDENCIES:\n  " + "\n  ".join(dangling)
+
+
+def warn_public_functions_without_category():
+    """Warn — never fail — on a public function carrying no `# CATEGORY`.
+
+    Bundled plugin and prompt internals will always lack one, so this
+    cannot be a hard failure; a genuinely new user-facing function going
+    undocumented still needs to be visible in CI output.
+    """
+    repo = Path(__file__).parent.parent
+    documented = set(_parsed_functions())
+    orphans = sorted(
+        p.stem
+        for p in (repo / "functions").glob("*.fish")
+        if not p.stem.startswith("_")
+        and p.stem not in documented
+        and "# SYNOPSIS" in p.read_text(encoding="utf-8")
+    )
+    if orphans:
+        print(f"  WARN  {len(orphans)} documented function(s) lack # CATEGORY:")
+        print("        " + ", ".join(orphans))
+
+
+def _without_section_5(text: str) -> str:
+    """Drop `# 5. FUNCTIONS REFERENCE` through the start of section 6.
+
+    Section 5 is generated from `functions/*.fish` headers, so it
+    legitimately differs from the pre-migration snapshot. The round-trip
+    guard covers the authored sections either side of it.
+    """
+    start = text.find("\n# 5. ")
+    if start == -1:
+        return text
+    end = text.find("\n# 6. ", start)
+    return text[:start] + (text[end:] if end != -1 else "")
 
 
 def _normalise(text: str) -> str:
@@ -128,6 +228,11 @@ def _normalise(text: str) -> str:
 def test_concat_roundtrips_original():
     """The concat of manual/ must reproduce the original fish-config.md exactly.
 
+    Section 5 is excluded: it is generated from `functions/*.fish` headers
+    and so legitimately differs from the snapshot. This test guarded the
+    *format* migration; the header-SSOT change is a *content* migration,
+    covered instead by the structural checks above.
+
     Prefers docs/fish-config.md.orig (a snapshot of the pre-migration file)
     when present. Once that snapshot is deleted post-migration,
     docs/fish-config.md IS the concat output regenerated in Step 5, so
@@ -149,8 +254,8 @@ def test_concat_roundtrips_original():
     if not original.exists():
         original = docs / "fish-config.md"
         label = "fish-config.md"
-    got = build_manual.build_concat(docs / "manual")
+    got = _without_section_5(build_manual.build_concat(docs / "manual"))
-    want = original.read_text()
+    want = _without_section_5(original.read_text())
     if got != want:
         norm_got = _normalise(got)
         norm_want = _normalise(want)
@@ -393,6 +498,7 @@ def main() -> int:
         except AssertionError as e:
             print(f"  FAIL  {t.__name__}: {e}", file=sys.stderr)
             failed += 1
+    warn_public_functions_without_category()
     print(f"\n{len(TESTS) - failed}/{len(TESTS)} passed")
     return 1 if failed else 0
 

functions/agy.fish

@@ -4,6 +4,9 @@
 # CATEGORY
 #   12-ai-and-developer-tools
 #
+# DEPENDENCIES
+#   agents-init
+#
 # SYNOPSIS
 #   agy [ARGS...]
 #

functions/claude.fish

@@ -4,6 +4,9 @@
 # CATEGORY
 #   12-ai-and-developer-tools
 #
+# DEPENDENCIES
+#   agents-init
+#
 # SYNOPSIS
 #   claude [ARGS...]
 #

functions/config-toggle.fish

@@ -4,6 +4,9 @@
 # CATEGORY
 #   14-miscellaneous
 #
+# DEPENDENCIES
+#   config-settings
+#
 # SYNOPSIS
 #   config-toggle [args...]
 #

functions/git-clean.fish

@@ -14,7 +14,6 @@
 #
 # ARGUMENTS
 #   -h, --help   Show help message
-#   -f, --force   Force-delete unmerged branches too
 #   -f, --force  Force-delete unmerged orphaned branches (git branch -D)
 #
 # RETURNS

functions/open-url.fish

@@ -39,8 +39,6 @@
 #   open-url -v https://fish-config-docs.pages.dev/
 #
 # NOTES
-#   Used internally by config-help --html.
-#
 #   Typo abbreviation: url-open (expands to open-url on space/enter).
 function open-url --description 'Open a URL in the best available web browser'
     argparse h/help s/silent v/verbose -- $argv

functions/repo-open.fish

@@ -4,6 +4,9 @@
 # CATEGORY
 #   14-miscellaneous
 #
+# DEPENDENCIES
+#   open-url
+#
 # SYNOPSIS
 #   repo-open [-p|--print] [-r|--root]
 #   repo-open --help