Fixing cmake dependencies and "make {install,clean}"

Also includes a bunch of cleanup.
Band-aid to get Broxygen's bif documentation back.

We'll need a different approach here eventually.
Removing debugging output.
Merge remote-tracking branch 'origin/master' into topic/robin/plugins

Thanks to git this merge was less troublesome that I was afraid it
would be. Not all tests pass yet though (and file hashes have changed
unfortunately).

Conflicts:
	cmake
	doc/scripts/DocSourcesList.cmake
	scripts/base/init-bare.bro
	scripts/base/protocols/ftp/main.bro
	scripts/base/protocols/irc/dcc-send.bro
	scripts/test-all-policy.bro
	src/AnalyzerTags.h
	src/CMakeLists.txt
	src/analyzer/Analyzer.cc
	src/analyzer/protocol/file/File.cc
	src/analyzer/protocol/file/File.h
	src/analyzer/protocol/http/HTTP.cc
	src/analyzer/protocol/http/HTTP.h
	src/analyzer/protocol/mime/MIME.cc
	src/event.bif
	src/main.cc
	src/util-config.h.in
	testing/btest/Baseline/coverage.bare-load-baseline/canonified_loaded_scripts.log
	testing/btest/Baseline/coverage.default-load-baseline/canonified_loaded_scripts.log
	testing/btest/Baseline/istate.events-ssl/receiver.http.log
	testing/btest/Baseline/istate.events-ssl/sender.http.log
	testing/btest/Baseline/istate.events/receiver.http.log
	testing/btest/Baseline/istate.events/sender.http.log
Merge branch 'topic/robin/plugins' of git.bro-ids.org:bro into topic/robin/plugins
Removing Broxygen's dpd_config magic.

The table doesn't exist anymore. The functionality has been replaced
with a function call but I can't really see how to get it out of
there. We could get it from the analyzer manager, however then we
can't tie it back to a script anymore. What we could do eventually is
add this to the information about the analyzer plugin.
Fix the issue with transaction ID reuse in a single DNS connection.

 - Each transaction ID within a connection is now maintained as
   a queue of DNS::Info logging records.

 - New function added to the queue.bro script to support
   peeking at the new gettable item in the queue without removing it.
Fixing Broxygen generation.

Needs to have BROMAGIC set to find the magic database.
Updating submodule(s).

 [nomail]
Merge remote-tracking branch 'origin/topic/seth/dns-dual-trans-id-fix'

Closes #1008.

* origin/topic/seth/dns-dual-trans-id-fix:
  Fix the issue with transaction ID reuse in a single DNS connection.
Fix uninitialized DPM member.

Was seeing crashes due to this primarily on Ubuntu 12.04 when
generating reST docs.
Merge remote-tracking branch 'origin/fastpath'

* origin/fastpath:
  Fix uninitialized DPM member.
change sqlite3 default threading mode to no-mutex, disable memory
statistics, finalize prepared statement before exitting logger.

This might fix the deadlock issue, at least it did not happen for
me on my tried on the test system where it happened quite regularly
before.
Updating submodule(s).

 [nomail]
Merge remote-tracking branch 'origin/fastpath'

* origin/fastpath:
  change sqlite3 default threading mode to no-mutex, disable memory statistics, finalize prepared statement before exitting logger.
(hopefully) fix mutex lock problem.

log writers were removed on shutdown while frontends still
had pointers to it.

A similar fix will be necessary for the input framework (tomorrow :) )
Merge remote-tracking branch 'origin/fastpath'

* origin/fastpath:
  (hopefully) fix mutex lock problem.
Fixing tests.

Part of this involves making the file-analysis tests independent of
specific hash values. I've done that only partially though.
Fixing test that would fail without ES/curl support.

It used to special-case an error message produced in the case that ES
isn't available, however with scripts/test-all-policy.bro now
explicitly disabling ES output, that doesn't seem necessary anymore.
File analysis framework interface simplifications.

- Remove script-layer data input interface (will be managed directly
  by input framework later).

- Only track files internally by file id hash.  Chance of collision
  too small to justify also tracking unique file string.