The Arduino Core uses Timer0 for timing Functions, if you need Timer0 T0 Pin for Measurement/External Triggering you can Switch the Timing to Timer2. This is a Variant set.
Copy The Files to your IDE Folder /hardware/Arduino/avr/variants/TNStandard
Change/Add Line in Boards.txt
Example1:
Change Line
uno.build.variant=standard
To
uno.build.variant=TNStandard
Example2(Creates new Menu for Both)
Delete Line
uno.build.variant=standard
Add Lines
uno.menu.cpu.Timer0=Timer0
uno.menu.cpu.Timer0.build.variant=standard
uno.menu.cpu.Timer1=Timer1
uno.menu.cpu.Timer1.build.variant=TNStandard