Fix for "output discrepancy if file already exists" (Issue #12)

[romangrothausmann]

Possible fix for Issue #12, please check.
Yields the correct dependencies for the example Makefile in these cases:

touch x.a
touch x.a x.b
touch x.a x.b x.z
touch x.b
touch x.z
touch x.a x.b x.z; rm x.a
touch x.a x.b x.z; rm x.z

but not in this:

touch x.a x.b x.z; rm x.b

[lindenb]

Thanks for your PR.
I tried your version with tabix : https://sourceforge.net/projects/samtools/files/tabix/

this is the output I get : https://github.com/lindenb/makefile2graph/blob/master/screenshot.png

and below is your output:

as you can see, your version contains many circular dependencies.

[romangrothausmann]

Hm, I'll have a look.
Do You think the general idea for the indentation parsing is implement sensibly?
At least, refering to #12, I figured, that it was not the Pruning file x.a but the Considering target file 'x.a'. issued before Considering target file 'x.b'. that caused the wrong dependency.

[romangrothausmann]

Using the same comparison as in L283 makes the output for both (#12 and tabix) look correct.

Even touch x.a x.b x.z; rm x.b is correct, I just was irritated by the disconnected x.a but as it exists and needs no updating, the output is right.

I'm just not sure whether an indentation condition should be added to other else if(startsWith(. Perhaps @deryni can comment on this.