Broken git process after checkout/clean

Hi all,

Please bear with me, as I'm not that l33t with programming and "gitting",
but I "débrouille" myself!

It appears I've broken my working tree and cannot configure/make anymore;
it all started when I tried to "git pull" yesterday and was greeted with
the following :

error: Your local changes to the following files would be overwritten by
> merge:
>         configure
> Please, commit your changes or stash them before you can merge.
> Aborting


This is what was given by "git status" :

# On branch master
> # Your branch is behind 'origin/master' by 63 commits, and can be
> fast-forwarded.
> #
> # Changes not staged for commit:
> #   (use "git add <file>..." to update what will be committed)
> #   (use "git checkout -- <file>..." to discard changes in working
> directory)
> #
> #       modified:   configure
> #       modified:   nsock/src/configure
> #
> # Untracked files:
> #   (use "git add <file>..." to include in what will be committed)
> #
> #       libssh2/lib/
> #       libssh2/libssh2.pc
> #       libssh2/libtool
> #       libssh2/src/.deps/
> #       libssh2/src/.libs/
> #       libssh2/src/libssh2_config.h
> #       libssh2/src/stamp-h1
> no changes added to commit (use "git add" and/or "git commit -a")


So I issued a "git checkout .", but also "git clean -df" to remove the
untracked files, and this is what I believe created the following issue :

cd libssh2/src && make libdir="/lib" prefix=""
> DESTDIR=/home/ionreflex/gitstuff/nmap/libssh2 install-libLTLIBRARIES;
> make[1]: Entering directory `/home/ionreflex/gitstuff/nmap/libssh2/src'
>  /bin/mkdir -p '/home/ionreflex/gitstuff/nmap/libssh2/lib'
>  /bin/bash ../libtool   --mode=install /usr/bin/install -c   libssh2.la
> '/home/ionreflex/gitstuff/nmap/libssh2/lib'
> libtool: install: /usr/bin/install -c .libs/libssh2.so.1.0.1
> /home/ionreflex/gitstuff/nmap/libssh2/lib/libssh2.so.1.0.1
> /usr/bin/install: cannot stat `.libs/libssh2.so.1.0.1': No such file or
> directory
> make[1]: *** [install-libLTLIBRARIES] Error 1
> make[1]: Leaving directory `/home/ionreflex/gitstuff/nmap/libssh2/src'
> make: *** [build-libssh2] Error 2


I believe it to be an issue with ".gitignore" or maybe those untracked
files were improperly added under revision control (!), this I don't know
(but I hope I'm clear enough!).

At first I thought maybe the problem was because I was trying to compile on
my BBB running wheezy32 (armv7l is 32bits... -_-), but I've reproduced the
same situation on an up-to-date CentOS7.

Lemme know if this is relevant and if I can be of any help, I'm currently
and often on IRC if you wish to chat directly.

Thank you,



Ion

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