Magically Created Files outside of /custom/

My installation magically has the following files all of the sudden in it which are outside of /custom/. I don’t where they came from and I was wondering if someone knew without me having to dig into the code.

        
        include/SugarEmailAddress/SugarEmailAddressLegacy.js
	modules/AOS_PDF_Templates/PDF_Lib/ttfontdata/dejavusanscondensed.cw.dat
	modules/AOS_PDF_Templates/PDF_Lib/ttfontdata/dejavusanscondensed.cw127.php
	modules/AOS_PDF_Templates/PDF_Lib/ttfontdata/dejavusanscondensed.mtx.php
	modules/AOS_PDF_Templates/PDF_Lib/ttfontdata/dejavusanscondensedB.cw.dat
	modules/AOS_PDF_Templates/PDF_Lib/ttfontdata/dejavusanscondensedB.mtx.php
	modules/Activities/OpenListView.php
	modules/Calendar/Dashlets/CalendarDashlet/CalendarDashlet.es_es.lang.php
	modules/Calendar/Dashlets/CalendarDashlet/CalendarDashlet.ru_ru.lang.php
	modules/Home/about.js
	modules/Studio/language/en_us.Portal.html

The reason for this being important is for my attempting to better manage this through VCS and deployment software.

Thanks.