docs(functions): merge remaining manual-only facts into headers

Word-level diff of every manual entry against its generated counterpart
surfaced 546 tokens present in the manual and absent from the header —
losses reconcile.py missed, because it compared description length and
these headers are longer overall thanks to ARGUMENTS/RETURNS.

Merged the substantive ones (546 -> 202 residual tokens, the remainder
being synonym drift). Notable real fixes:

- git-clean: -f/--force was missing from ARGUMENTS entirely
- pkg: per-package-manager query table
- qc: cli-role rationale, role paths, --role passthrough
- config-help: site URL, xdg-open, man page path, case-insensitivity
- agents-init: idempotency, .gitignore paths, upstream pull, wrapper callers
- smart_exit: exit-builtin wiring note, $SCROLLBACK_HISTORY_DIR

The manual's claim that claude/agy pass `agents-init --agents` is stale;
both pass `--quiet` (full setup). Header wins, manual dropped.

functions/smart_exit.fish

@@ -8,9 +8,10 @@
 #   smart_exit [-h] [-n]
 #
 # DESCRIPTION
-#   Closes the shell session, capturing and archiving the terminal scrollback
-#   log before exit (Kitty only). Automatically prunes junk and excess log
-#   files according to $SCROLLBACK_HISTORY_MAX_FILES.
+#   Closes the shell session. In Kitty, captures the terminal scrollback to a
+#   timestamped log file in $SCROLLBACK_HISTORY_DIR before exiting.
+#   Automatically prunes junk and the oldest logs when the count exceeds
+#   $SCROLLBACK_HISTORY_MAX_FILES.
 #
 # ARGUMENTS
 #   -h, --help    Show help message
@@ -21,7 +22,12 @@
 #   1  Argument parsing failed
 #
 # EXAMPLE
+#   smart_exit
 #   smart_exit --no-log
+#
+# NOTES
+#   The exit builtin is wired to smart_exit for interactive sessions. Typing
+#   `exit` or Ctrl+D behaves identically to calling smart_exit directly.
 function smart_exit --description 'Capture colorized scrollback before exiting, with pruning and safe overrides'
     # Opinionated guard (C3): exit plainly when overrides are disabled.
     # This composes with Task #4's __fish_config_enable_logging, which will