git with included git repo with master branch in ../_deploy dir is not cloned from github pages blog

gistfile1.txt

peterv@ASUS:~/data/temp/github/petervandenabeele$ git clone git@github.com:petervandenabeele/petervandenabeele.github.com.git
Initialized empty Git repository in /home/peterv/data/temp/github/petervandenabeele/petervandenabeele.github.com/.git/
remote: Counting objects: 4084, done.
remote: Compressing objects: 100% (1438/1438), done.
remote: Total 4084 (delta 2327), reused 4064 (delta 2307)
Receiving objects: 100% (4084/4084), 997.31 KiB | 232 KiB/s, done.
Resolving deltas: 100% (2327/2327), done.

peterv@ASUS:~/data/temp/github/petervandenabeele$ ls -l
total 4
drwxr-xr-x 8 peterv peterv 4096 2012-01-11 00:01 petervandenabeele.github.com

peterv@ASUS:~/data/temp/github/petervandenabeele$ cd petervandenabeele.github.com/

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ git branch
* master

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ ls -al
total 208
drwxr-xr-x 8 peterv peterv  4096 2012-01-11 00:01 .
drwxr-xr-x 3 peterv peterv  4096 2012-01-11 00:01 ..
drwxr-xr-x 3 peterv peterv  4096 2012-01-11 00:01 assets
-rw-r--r-- 1 peterv peterv 76249 2012-01-11 00:01 atom.xml
drwxr-xr-x 5 peterv peterv  4096 2012-01-11 00:01 blog
-rw-r--r-- 1 peterv peterv    23 2012-01-11 00:01 CNAME
-rw-r--r-- 1 peterv peterv   400 2012-01-11 00:01 favicon.png
drwxr-xr-x 8 peterv peterv  4096 2012-01-11 00:01 .git
drwxr-xr-x 2 peterv peterv  4096 2012-01-11 00:01 images
-rw-r--r-- 1 peterv peterv 81279 2012-01-11 00:01 index.html
drwxr-xr-x 3 peterv peterv  4096 2012-01-11 00:01 javascripts
-rw-r--r-- 1 peterv peterv   801 2012-01-11 00:01 sitemap.xml
drwxr-xr-x 2 peterv peterv  4096 2012-01-11 00:01 stylesheets

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ git checkout -t origin/source
Branch source set up to track remote branch source from origin.
Switched to a new branch 'source'

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ ls -al
total 92
drwxr-xr-x 7 peterv peterv  4096 2012-01-11 00:02 .
drwxr-xr-x 3 peterv peterv  4096 2012-01-11 00:01 ..
-rw-r--r-- 1 peterv peterv  1303 2012-01-11 00:02 CHANGELOG.markdown
-rw-r--r-- 1 peterv peterv    23 2012-01-11 00:01 CNAME
-rw-r--r-- 1 peterv peterv   349 2012-01-11 00:02 config.rb
-rw-r--r-- 1 peterv peterv   632 2012-01-11 00:02 config.ru
-rw-r--r-- 1 peterv peterv  2844 2012-01-11 00:02 _config.yml
-rw-r--r-- 1 peterv peterv   304 2012-01-11 00:02 Gemfile
-rw-r--r-- 1 peterv peterv  1275 2012-01-11 00:02 Gemfile.lock
drwxr-xr-x 8 peterv peterv  4096 2012-01-11 00:02 .git
-rw-r--r-- 1 peterv peterv   163 2012-01-11 00:02 .gitignore
drwxr-xr-x 2 peterv peterv  4096 2012-01-11 00:02 plugins
-rw-r--r-- 1 peterv peterv 15102 2012-01-11 00:02 Rakefile
-rw-r--r-- 1 peterv peterv    11 2012-01-11 00:02 .rbenv-version
-rw-r--r-- 1 peterv peterv  2730 2012-01-11 00:02 README.markdown
-rw-r--r-- 1 peterv peterv    28 2012-01-11 00:02 .rvmrc
drwxr-xr-x 5 peterv peterv  4096 2012-01-11 00:02 sass
-rw-r--r-- 1 peterv peterv    20 2012-01-11 00:02 .slugignore
drwxr-xr-x 9 peterv peterv  4096 2012-01-11 00:02 source
drwxr-xr-x 3 peterv peterv  4096 2012-01-11 00:02 .themes

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ vim source/_posts/2011-11-26-installing-ruby-and-rails-with-rvm-on-ubuntu-11-dot-10.markdown 
peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ # changed one space

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ bundle install
Fetching source index for http://rubygems.org/
Using rake (0.9.2.2) 
Installing RedCloth (4.2.8) with native extensions 
Installing posix-spawn (0.3.6) with native extensions 
Installing albino (1.3.3) 
Installing blankslate (2.1.2.4) 
Installing chunky_png (1.2.1) 
Installing fast-stemmer (1.0.0) with native extensions 
Installing classifier (1.3.3) 
Installing fssm (0.2.7) 
Installing sass (3.1.5) 
Installing compass (0.11.5) 
Installing directory_watcher (1.4.0) 
Installing ffi (1.0.9) with native extensions 
Installing haml (3.1.2) 
Installing kramdown (0.13.3) 
Installing liquid (2.2.2) 
Installing syntax (1.0.0) 
Installing maruku (0.6.0) 
Installing jekyll (0.11.0) 
Installing rubypython (0.5.1) 
Installing pygments.rb (0.1.3) 
Installing rack (1.3.2) 
Installing rb-fsevent (0.4.3.1) with native extensions 
Installing rdiscount (1.6.8) with native extensions 
Installing rubypants (0.2.0) 
Installing tilt (1.3.2) 
Installing sinatra (1.2.6) 
Installing stringex (1.3.0) 
Using bundler (1.0.21) 
Your bundle is complete! Use `bundle show [gemname]` to see where a bundled gem is installed.

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ rake generate
## Generating Site with Jekyll
directory source/stylesheets/ 
   create source/stylesheets/screen.css 
/home/peterv/.rvm/gems/ruby-1.9.3-p0/gems/maruku-0.6.0/lib/maruku/input/parse_doc.rb:22:in `<top (required)>': iconv will be deprecated in the future, use String#encode instead.
Configuration from /home/peterv/data/temp/github/petervandenabeele/petervandenabeele.github.com/_config.yml
/home/peterv/.rvm/gems/ruby-1.9.3-p0/gems/ffi-1.0.9/lib/ffi/platform.rb:27: Use RbConfig instead of obsolete and deprecated Config.
Building site: source -> public
Successfully generated site: source -> public

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ rake deploy
## Deploying branch to Github Pages 

## copying public to _deploy
cp -r public/. _deploy
cd _deploy
The following paths are ignored by one of your .gitignore files:
_deploy
Use -f if you really want to add them.
fatal: no files added  ##### NOTE by @peter_v  ##### FAIL !!!

## Commiting: Site updated at 2012-01-10 23:05:00 UTC
# On branch source
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   ../source/_posts/2011-11-26-installing-ruby-and-rails-with-rvm-on-ubuntu-11-dot-10.markdown
#
no changes added to commit (use "git add" and/or "git commit -a")

## Pushing generated _deploy website
Everything up-to-date

## Github Pages deploy complete
cd -

### NOTE by @peter_v ... everything is success, but nothing happened ...
### It tooks me weeks to understand what was going on here ...
### Also see https://github.com/imathis/octopress/issues/336


peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com$ cd _deploy/

peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com/_deploy$ ls -al # NO .git repo here
total 204
drwxr-xr-x  7 peterv peterv  4096 2012-01-11 00:05 .
drwxr-xr-x 11 peterv peterv  4096 2012-01-11 00:05 ..
drwxr-xr-x  3 peterv peterv  4096 2012-01-11 00:05 assets
-rw-r--r--  1 peterv peterv 76249 2012-01-11 00:05 atom.xml
drwxr-xr-x  5 peterv peterv  4096 2012-01-11 00:05 blog
-rw-r--r--  1 peterv peterv    23 2012-01-11 00:05 CNAME
-rw-r--r--  1 peterv peterv   400 2012-01-11 00:05 favicon.png
drwxr-xr-x  2 peterv peterv  4096 2012-01-11 00:05 images
-rw-r--r--  1 peterv peterv 81279 2012-01-11 00:05 index.html
drwxr-xr-x  3 peterv peterv  4096 2012-01-11 00:05 javascripts
-rw-r--r--  1 peterv peterv   801 2012-01-11 00:05 sitemap.xml
drwxr-xr-x  2 peterv peterv  4096 2012-01-11 00:05 stylesheets


peterv@ASUS:~/data/temp/github/petervandenabeele/petervandenabeele.github.com/_deploy$ git status # this is the "top" branch
# On branch source
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   ../source/_posts/2011-11-26-installing-ruby-and-rails-with-rvm-on-ubuntu-11-dot-10.markdown
#
no changes added to commit (use "git add" and/or "git commit -a")