Support TIMER1C

Some devices, such as the atmega2560 or the atmega256rfr2 have a timer1c
output. It seems this output is not connected to anything on the Arduino
Mega, but this allows using it on third party hardware nonetheless.
Allow variants to define an initVariant() function that is called at startup.

See #2080
Unconfuse error message

When a core directory without boards.txt file was encountered, the IDE
would show:

	Could not find boards.txt in /path/to/core/boards.txt.  Is it pre-1.5?

Which appears confusing: Is it looking inside a directory called
boards.txt? Now this is improved to:

	Could not find boards.txt in /path/to/core/.  Is it pre-1.5?

which makes a lot more sense.
Don't include .o files from the variant in core.a

If a variant supplied source files, these would be included in core.a
before. However, object files from core.a would only actually be
included in the build if they supplied a symbol for a strong reference
that was still missing.

In practice, this meant that a variant source file that only defines
interrupt handlers, or only defines strong versions of functions that
already had weak versions available, was not included.

By moving the variant .o files out of core.a and including them in the
build directly, this problem is solved.

Furthermore, the compilation of variant files is moved to after the
generation of core.a, to make it clearer in the code and verbose output
what is now happening.
Allow variants to define an initVariant() function that is called at startup.

See #2080 and #2139.
initVariant() is now declared as external "C" function.

See #2080 for more details.
Merge pull request #2139 from cmaglie/init-variant

Allow variants to define an initVariant() function that is called at startup
Updated revision log
Merge branch 'ide-1.5.x-timer-variant' of github.com:matthijskooijman/Arduino into matthijskooijman-ide-1.5.x-timer-variant
Merge branch 'master' into matthijskooijman-ide-1.5.x-timer-variant

Conflicts:
	app/src/processing/app/debug/Compiler.java
	hardware/arduino/sam/cores/arduino/main.cpp
Updated gitignore