Moving to autotools standard layout

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+### backupninja mysql config file ###
+
+databases   = all
+backupdir   = /var/backups/mysql
+hotcopy     = no
+sqldump     = yes
+compress    = yes
+
+### authentication ###
+
+# three authentication methods:
+#
+# 1. setting the user, so that /home/user/.my.cnf is used.
+# user = some-unix-user
+#
+# 2. specifying the mysql dbuser and dbpassword,
+#    which generates a temporary .my.cnf in /root/.my.cnf
+# dbusername  = <some-mysql-user>
+# dbpassword  = <password>
+#
+# 3. specify which config file to use with configfile
+#    (this option does not work with hotcopy)
+# configfile = /etc/mysql/debian.cnf
+#
+# if user and dbusername are not specified, the default is to use
+# /etc/mysql/debian.cnf for configfile.
+
+### all options ###
+
+# configfile = < path/to/file > (default = /etc/mysql/debian.cnf)
+# The config file is passed to mysql with --defaults-file.
+# On debian, this default will allow backupninja to make backups
+# of mysql without configuring any additional options. 
+# (this option is not compatible with "user" or "dbusername").
+#
+# user = <user> (default = root)
+# Run mysql commands as 'user'. A valid .my.cnf must exist with a 
+# database username and password in the user's home directory.
+# (this option is not compatible with "configfile" or "dbusername").
+#
+# dbusername = <dbuser> (no default)
+# The user must have access to the databases specified later.
+# (this option is not compatible with "configfile" or "user").
+#
+# dbpassword = <dbpass> (no default)
+# The password used with dbusername. this password will NOT be passed 
+# on the command line and is not readable using "ps aux".
+#
+# dbhost = <host> (default = localhost)
+# only localhost works right now.
+#
+# databases = < all | db1 db2 db3 > (default = all)
+# which databases to backup. should either be the word 'all' or a 
+# space separated list of database names.
+#
+# backupdir = < path/to/destination > (default = /var/backups/mysql)
+# where to dump the backups. hotcopy backups will be in a subdirectory 'hotcopy' and
+# sqldump backups will be in a subdirectory 'sqldump'
+#
+# hotcopy = < yes | no > (default = no)
+# make a backup of the actual database binary files using mysqlhotcopy.
+#
+# sqldump = < yes | no > (default = no)
+# make a backup using mysqldump. this creates text files with sql commands
+# sufficient to recontruct the database.
+#
+# compress = < yes | no > (default = yes)
+# if yes, compress the sqldump output. 
+#
+# vsname = <vserver> (no default)
+# what vserver to operate on, only used if vserver = yes in /etc/backupninja.conf
+# if you do not specify a vsname the host will be operated on
+# 
+# NB: databases = all doesn't seem to work with hotcopy = yes when vsname is specified
+# I would like to know how to fix this.