Hello Aprelium,
Long time no see. Anyway, I noticed something possibly amiss with the 2.9.0.1 version of Abyss. My URL Rewrites used to work in previous versions of Abyss and these things are pretty straightforward, as much as I can understand them.
These are my key .htaccess constraints.

  RewriteCond %{REQUEST_FILENAME} !-f
  RewriteCond %{REQUEST_FILENAME} !-d
  RewriteCond %{REQUEST_URI} !=/favicon.ico
  RewriteRule ^ index.php [L]

I then made up my Abyss URL Rewrite rules and these are what I got from the debugging logs. Next, I browsed for https://192.168.10.60/sandbox/cenmap/?q=welcome_census_mapping_submission_facility - which is a Drupal-based project of mine.
Note that these logs have been redacted for hopefully easier reading :-).

Request URI=[/sandbox/cenmap/]:
		SERVER_SOFTWARE=Abyss/2.9.0.1-X1-Win32 AbyssLib/2.9.0.0
		REQUEST_URI=/sandbox/cenmap/?q=welcome_census_mapping_submission_facility
		URL=/sandbox/cenmap/?q=welcome_census_mapping_submission_facility
		SCRIPT_URL=/sandbox/cenmap/?q=welcome_census_mapping_submission_facility
		SCRIPT_NAME=/sandbox/cenmap/
		SCRIPT_FILENAME=sandbox/cenmap/
		REQUEST_FILENAME=sandbox/cenmap/
		QUERY_STRING=q=welcome_census_mapping_submission_facility
		CONTENT_LENGTH=0

Rule #1: Regex [^\/sandbox\/cenmap\/(.*)$] matches with the request URI
		Testing the conditions:
			REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/]) expanded from [sandbox/cenmap/]) is not an empty fileFALSE
		The conditions are not verified (FALSE).
	Rule #2: Regex [^\/sandbox\/cenmap\/(.*)$] matches with the request URI
		Testing the conditions:
			REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/]) expanded from [sandbox/cenmap/]) is not a fileTRUE
			REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/]) expanded from [sandbox/cenmap/]) is not	a directoryTRUE
			REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/]) expanded from [sandbox/cenmap/]) is an empty fileTRUE
			REQUEST_URI (value: [C:\Websites\default_https//sandbox/cenmap/?q=welcome_census_mapping_submission_facility]) expanded from [/sandbox/cenmap/?q=welcome_census_mapping_submission_facility]) is not a fileTRUE
			REQUEST_URI (value: [C:\Websites\default_https//sandbox/cenmap/?q=welcome_census_mapping_submission_facility]) expanded from [/sandbox/cenmap/?q=welcome_census_mapping_submission_facility]) is not	a directoryTRUE
			REQUEST_URI (value: [C:\Websites\default_https//sandbox/cenmap/?q=welcome_census_mapping_submission_facility]) expanded from [/sandbox/cenmap/?q=welcome_census_mapping_submission_facility]) is an empty fileTRUE
			QUERY_STRING (value: [q=welcome_census_mapping_submission_facility]) does not match with [^q=.*] => FALSE
				Matching results:
					%0=q=welcome_census_mapping_submission_facility
	Last condition is FALSE. Validation of next conditions is useless.
	 ===> No rule matches.

----------------------------------------------
Request URI=[/sandbox/cenmap/misc/jquery.js]:
		REQUEST_URI=/sandbox/cenmap/misc/jquery.js?v=1.4.4
		URL=/sandbox/cenmap/misc/jquery.js?v=1.4.4
		SCRIPT_URL=/sandbox/cenmap/misc/jquery.js?v=1.4.4
		SCRIPT_NAME=/sandbox/cenmap/misc/jquery.js
		SCRIPT_FILENAME=sandbox/cenmap/misc/jquery.js
		REQUEST_FILENAME=sandbox/cenmap/misc/jquery.js
		QUERY_STRING=v=1.4.4
		CONTENT_LENGTH=0

Rule #1: Regex [^\/sandbox\/cenmap\/(.*)$] matches with the request URI
		Testing the conditions:
			REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is not an empty fileFALSE
		The conditions are not verified (FALSE).
	Rule #2: Regex [^\/sandbox\/cenmap\/(.*)$] matches with the request URI
		Testing the conditions:
			REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is not a fileTRUE
			REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is not	a directoryTRUE
			REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is an empty fileTRUE
			REQUEST_URI (value: [C:\Websites\default_https//sandbox/cenmap/misc/jquery.js?v=1.4.4]) expanded from [/sandbox/cenmap/misc/jquery.js?v=1.4.4]) is not a fileTRUE
			REQUEST_URI (value: [C:\Websites\default_https//sandbox/cenmap/misc/jquery.js?v=1.4.4]) expanded from [/sandbox/cenmap/misc/jquery.js?v=1.4.4]) is not	a directoryTRUE
			REQUEST_URI (value: [C:\Websites\default_https//sandbox/cenmap/misc/jquery.js?v=1.4.4]) expanded from [/sandbox/cenmap/misc/jquery.js?v=1.4.4]) is an empty fileTRUE
			QUERY_STRING (value: [v=1.4.4]) does not match with [^q=.*] => TRUE
			SCRIPT_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is not a fileTRUE
			SCRIPT_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is not	a directoryTRUE
			SCRIPT_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is an empty fileTRUE
		All the conditions are verified (TRUE).
	Matching results:
		$0=/sandbox/cenmap/misc/jquery.js
		$1=misc/jquery.js
	Replacing the virtual path with [/sandbox/cenmap/] => /sandbox/cenmap/
	Adding the query string replacement [?q=$1] => /sandbox/cenmap/?q=misc/jquery.js
	 ===> Internal redirection to /sandbox/cenmap/?q=misc/jquery.js

Here are my concerns from the above situation.
1. On the 1st section, where URL=/sandbox/cenmap/?q=welcome_census_mapping_submission_facility, I am hence asking why this section has been entitled in its first line as:

Request URI=[/sandbox/cenmap/]:

whereas in the actual variables,

REQUEST_URI=/sandbox/cenmap/?q=welcome_census_mapping_submission_facility

is being displayed. This makes for a confusing debugging log tracing activity. Would you please make the section title congruent with the actual variable?
2. Moving on to the next section where REQUEST_URI=/sandbox/cenmap/misc/jquery.js?v=1.4.4. Note that this object (jquery.js) is an actual file sitting on my server "2014/01/16 03:43 AM 78,602 jquery.js". However, on Rule#2 under this same section, we see:

REQUEST_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is not a fileTRUE

- which, I believe is incorrect. REQUEST_FILENAME is the relevant rewrite condition variable in my .htaccess file.
I am also wondering on the validity of the following test conditions:

			SCRIPT_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is not a fileTRUE
			SCRIPT_FILENAME (value: [C:\Websites\default_https/sandbox/cenmap/misc/jquery.js]) expanded from [sandbox/cenmap/misc/jquery.js]) is an empty fileTRUE

Am I correct in my assessment on this situation? Is this a manifestation of bugs in Abyss 2.9.0.1? Or am I implementing my rewrites and reading these logs wrongly? Kindly provide useful insights. Thanks!