Merge pull request #517 in SNORT/snort3 from appid_port_ws1_merge_this to master

Merge pull request #517 in SNORT/snort3 from appid_port_ws1_merge_this to master

Squashed commit of the following:

commit b53b7f1d5e5c5249515b25b7db35f65cdbeebe71
Author: davis mcpherson <davis.mcpherson@gmail.com>
Date:   Thu Jun 9 11:50:39 2016 -0400

    initial prep work to port appid to snort++
    initial work to get dns/smtp detectors working and cleanup of many issues left from initial prep of appid
    search tool unit tests
    Moved AM_CPPFLAGS change into appid specific Makefile.am files.
    fixed compiler warnings
    fixed formating issues, misc minor code review nits
    Fix cmake problems and warnings.
    use REMOVED_WHILE_NOT_IN_USE for all code #ifdef'ed out for porting issues
    change patterns defined by const char* to const char array
    init net_list_by_zone array to 0
    initialize all array member variables to nullptr
    initial net list by zone array to nullptr
    free memory allocated by snort_strdup for module config strings
    AppIdModuleConfig is now a class not a struct
    for now use snort_free instead of delete
    no defaults for appid detector dir and thirdparty dir
    init member variables for AppIdData
    free memory allocated for AppIdData member variables
    initialize ALL member variables of AppIdData class
    move functions called to free memory in AppIdData to the AppIdData class
    source formating issue, fix type mismatch on debug print specifier for IpProtocol