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fixing permissions

Is there a good way to get file permission changes into ones source package 
automaticly ?

This is my scenario: I have rebuilt the build system for the package ketm to 
automake/autoconf. This has generated a new configure file. So far so good. 

Problem is that the diff from the original source doesn't include file 
permissions. So when porters/build robots try build the package this happends

extracting original source code
patching original code using ketm_0.0.6-1.diff.gz
trying to run ./configure 
/bin/sh: ./configure: /bin/sh: bad interpreter: Permission denied

I could fix the problem by manually by adding a chmod +x ./configure 
somewhere in the rules section. But manually adding a diff seems somewhat 

Magnus Ekdahl +46-(0)739-287181
public key available at http://oxtan.campus.luth.se/magnus.public
Key fingerprint = 18DE CB62 8A86 374E 824E  09ED 1987 4B18 1213 79F6

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