Renaming the default loaded "init" scripts and added command line arg for "bare-mode"

- bro.init was renamed to base/init-bare.bro and base/all.bro
  was renamed to init-default.bro.

- To run in "bare mode" with only the init-bare.bro and no other
  scripts from base/, use either -b or --bare-mode.

- The environment variable to run in "bare mode" has been removed.

scripts/base/init-default.bro

@@ -0,0 +1,41 @@
+##! This script loads everything in the base/ script directory.  If you want
+##! to run Bro without all of these scripts loaded by default, you can use
+##! the -b (--bare-mode) command line argument.  You can also copy the "@load"
+##! lines from this script to your own script to load only the scripts that 
+##! you actually want.
+
+@load base/utils/site
+@load base/utils/addrs
+@load base/utils/conn-ids
+@load base/utils/directions-and-hosts
+@load base/utils/files
+@load base/utils/numbers
+@load base/utils/paths
+@load base/utils/patterns
+@load base/utils/strings
+@load base/utils/thresholds
+
+# This has some deep interplay between types and BiFs so it's 
+# loaded in base/init-bare.bro
+#@load base/frameworks/logging
+@load base/frameworks/notice
+@load base/frameworks/dpd
+@load base/frameworks/signatures
+@load base/frameworks/packet-filter
+@load base/frameworks/software
+@load base/frameworks/intel
+@load base/frameworks/metrics
+@load base/frameworks/communication
+@load base/frameworks/control
+@load base/frameworks/cluster
+@load base/frameworks/reporter
+
+@load base/protocols/conn
+@load base/protocols/dns
+@load base/protocols/ftp
+@load base/protocols/http
+@load base/protocols/irc
+@load base/protocols/smtp
+@load base/protocols/ssh
+@load base/protocols/ssl
+@load base/protocols/syslog