File/IO readlines supporting new params limit, and open mode (thanks jose!)

Restore $! when catching exception.  In most cases jnr-posix on an error will throw and not get caught like this.   This is a special case and without significant changes jnr-posix this looks like the best fix to me.

It seems that www.amazon.com changed the CA cert it uses for its
ssl connection, and that caused us to start failing tests. After
some investigation, I figured out which cert we needed and what
the filename needed to be in the ca_path test. I have added a
README.txt to the ca_path and comments to all the related certs.
I also removed a cert file that appeared to be duplicate and added
a more explicitly incorrect cert for the test that is supposed to
fail verification.

This should fix jruby#653. We may catch too much here, but it seems
the intent of the rescue block was to capture most exceptions. It
also would have caught the ant ExitStatusException as a
NativeException before, but that stopped working after we stopped
wrapping Java exceptions. The fix should catch it properly now.

…ease? to cast NullPointerException

This reverts commit 05de78e.

…ame time

… RegexpError

…h_offset

IO.binwrite doesn't truncate the file if an offset is given

…x until 9k)

…exit status

…specs

Refactored directed graph specs

…f this)

Conflicts:
	.classpath
	nbproject/project.xml