Some folders were copied to DITA-OT's root directory

[jelovirt]

Converted from SourceForge issue 1304545, submitted by wuzhiq

When the dita files under input directory refer to some
files outside of input direcories, these directories
will be generated outside temp directory, which may
mistaken overide directories with same name.

[jelovirt]

Submitted by wuzhiq

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user_id=1231479

This problem will be fixed in release 1.2.

[jelovirt]

Submitted by wuzhiq

Logged In: YES
user_id=1231479

This problem has been fixed, now in the first step in
preprocess, the toolkit will try to parse the common root
directory for all the input files, and use it for later
processing.