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/pkg.fish

@@ -13,6 +13,14 @@
 #   In auto mode (no flag), detects whether each package is installed and
 #   toggles it — installing if absent, removing if present.
 #
+#   The package-installed check uses the correct query for each manager:
+#
+#     pacman/paru/yay  pacman -Qi
+#     apt              dpkg -s
+#     dnf/zypper/yum   rpm -q
+#     brew             brew list
+#     pkg              pkg info
+#
 # ARGUMENTS
 #   -h, --help       Show help message
 #   -i, --install    Force install mode