Various changes to documentation framework.

- Reorganize top-level 'doc' Makefile target so submodules can easily
  add their own doc-generating routines to it.  e.g. the Bro project
  makes a placeholder 'doc' target, then adds 'restdoc', 'sphinxdoc';
  later Broccoli can add it's own target as a dependency for generating
  API docs.

- Fixed generated docs for BIFs not being organized under a base/
  subdirectory like the original source files.

- Fixed documentation style for function parameters not applying to
  functions declared as record fields.

- Misc. script documentation tweaks to address warnings given by Sphinx.

scripts/base/init-bare.bro

@@ -1382,8 +1382,9 @@ const enable_syslog = F &redef;
 const peer_description = "bro" &redef;
 
 ## If true, broadcast events/state received from one peer to other peers.
-## NOTE: These options are only temporary. They will disappear when we get a
-## more sophisticated script-level communication framework.
+##
+## .. note:: These options are only temporary. They will disappear when we get
+##    a more sophisticated script-level communication framework.
 const forward_remote_events = F &redef;
 ## See :bro:id:`forward_remote_events`
 const forward_remote_state_changes = F &redef;
@@ -1513,6 +1514,6 @@ const skip_http_data = F &redef;
 ## UDP tunnels. See also: udp_tunnel_port, policy/udp-tunnel.bro.
 const parse_udp_tunnels = F &redef;
 
-## Load the logging framework here because it uses fairly deep integration with 
-## BiFs and script-land defined types.
+# Load the logging framework here because it uses fairly deep integration with 
+# BiFs and script-land defined types.
 @load base/frameworks/logging