added
--all-output
--pattern
--no-stop
removed --verbose/-v
put color in the pattern comments
updated paths to pattern files to either base64_patterns, or definitions
scan function has been broken up into a multiple functions which should make it more modular if future scan types are needed.
--comment, -a flag was added which prints the first comment to appear prior to the matched pattern in the pattern file.
--Fixed a bug with the out function. Previous updates of mine did not update all calls to the out function which I changed the parameters for. Fixed this by replacing the out function with an 'error' function.
--Alphabetized function definitions and did some general tidying up
--Made all functions private except the constructor.
--Created parseArgs function to handle reading in options.
--Fixed a bug with 'extra-check' where htaccess and googleBot were being pushed to the pattern array each time a file was scanned.
This bug was created when I moved the pattern initialize code to the constructor. Moved extra-check code with the rest of the initialize pattern calls.
--Added -no-color, -time, and -checksum flags. I'd prefer if the output was only as spammy as the user requests. Time should be helpful in tracing when the attack occurred and if files are related to the same hack. Time and checksum do not display by default. no-color flag makes it easier to dump to plain text files.
checking for comments and whitespace lines in pattern files should only be done once when the patterns are loaded.
Added this code to the loadPatterns() function and removed it from the 3 scan loops.
Verbose flag was not proceeding with the next scan due to !found being set. Added a check to see if it is verbose when it decides to do the next scan.
Patterns should be loaded once and only once. The files aren't large so not a problem with memory, however it might impact performance if we are loading the same 3 files ever time we scan a file.
