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I always think I solved the problem by chance. So I go back to think the
reason why the old repo code configured failed. It is not possible to cause
the problem by the renamed path and the branch of libreoffice-5-0-6. Over
the next three days, there was no progress on this matter. An accidental
opportunity, I found different unstaged changes in unmodified code repo by
using "git status" in cygwin and gitshell. The version of gitshell is "git
version 2.8.1.windows.1". Then I clone one code repo by cygwin, another one
by gitshell. The cygwin cloned code is going right. But the gitshell cloned
code will lead to errors as follow:

1、
$ ./autogen.sh --with-external-tar=/cygdrive/d/sources/lo-externalsrc
--with-junit=/cygdrive/d/sources/junit-4.10.jar
--with-ant-home=/cygdrive/d/sources/apache-ant-1.9.5 --enable-pch
--disable-ccache --enable-debug
./autogen.sh: line 1: $':\r': command not found
Running ./configure with
'--with-external-tar=/cygdrive/d/sources/lo-externalsrc
--with-junit=/cygdrive/d/sources/junit-4.10.jar
--with-ant-home=/cygdrive/d/sou --srcdir=/cygdrive/d/sources/libo-wingit
--enable-option-checking=fatal'
configure: error: invalid feature name: debug
Error running configure at ./autogen.sh line 281.

use commands as follow to pass this error
$ dos2unix autogen.sh
dos2unix: converting file autogen.sh to Unix format...
$ dos2unix config.sub
dos2unix: converting file config.sub to Unix format...
$ dos2unix config.guess
dos2unix: converting file config.guess to Unix format...

2、
cygpath: cannot create short name of 12.0\VC\Include
realpath: '12.0/VC': No such file or directory
configure: WARNING: realpath failed for "12.0/VC", not necessarily a
problem.
checking the dependency generation prefix (cl.exe -showIncludes)...
configure: error: cannot determine the -showIncludes prefix

use commands as follow to pass this error
shift+reset, go to the safe mode, do this: 
fsutil 8dot3name set c: 0 
fsutil file setshortname "Program Files (x86)" PROG~1 
fsutil file setshortname "Microsoft Visual Studio 12.0" msvc~120 
fsutil file setshortname "Windows Kits" W~Kits 

The shortname is unreadable as Tor Lillqvist-2 said. I will use better name
next time.

3、
checking whether to create huge library... no
checking whether to create hardlinks for delivering files... no
checking whether to use icerun wrapper... no
checking MPL subset... no restrictions
configure: setting up the build environment variables...
configure: creating ./config.status
.in'ig.status: error: cannot find input file: `config_host.mk
Error running configure at ./autogen.sh line 281.

There's nothing I can do about this.

Why the code cloned by cygwin and gitshell has different result of
configure. I open the same filename in different repo by UltraEdit. It shows
the difference. The cygwin cloned code is unix format, and the gitshell
cloned code is dos format.
Yes, the first problem and the third problem are caused by the dos format
files cloned by  the gitshell .





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