[chef] site installing tomcat cookbook git deleted files from my java cookbook

hi. is this expected? maybe it's something i don't understand about git
and git branching and community cookbooks.

long ago i had done "knife cookbook site install java", and committed
that cookbook to my own git repo. over time, i modifed that java
cookbook (added some templates, modifed the default recipe).

just now i did a "knife cookbook site install tomcat", and doing so
whacked my mods to the java cookbook.

whaaa? what to do?

thanks,
kallen


01/11 
02:
 
 ]$ knife cookbook site install tomcat
Installing tomcat to /home/kallen/sbox/ops/chef-repo/cookbooks
Checking out the master branch.
Creating pristine copy branch chef-vendor-tomcat
Downloading tomcat from the cookbooks site at version 0.10.3 to 
/home/kallen/sbox/ops/chef-repo/cookbooks/tomcat.tar.gz
Cookbook saved: /home/kallen/sbox/ops/chef-repo/cookbooks/tomcat.tar.gz
Removing pre-existing version.
Uncompressing tomcat version /home/kallen/sbox/ops/chef-repo/cookbooks.
removing downloaded tarball
1 files updated, committing changes
Creating tag cookbook-site-imported-tomcat-0.10.3
Checking out the master branch.
Updating 4046342..5863ea6
Fast-forward
 chef-repo/cookbooks/tomcat/README.md               |   56 +++++++
 chef-repo/cookbooks/tomcat/attributes/default.rb   |   59 ++++++++
 chef-repo/cookbooks/tomcat/metadata.rb             |   16 ++
 chef-repo/cookbooks/tomcat/recipes/default.rb      |   78 ++++++++++
 .../tomcat/templates/default/default_tomcat6.erb   |   64 ++++++++
 .../tomcat/templates/default/server.xml.erb        |  155 
++++++++++++++++++++
 .../tomcat/templates/default/sysconfig_tomcat6.erb |   59 ++++++++
 7 files changed, 487 insertions(+), 0 deletions(-)
 create mode 100644 chef-repo/cookbooks/tomcat/README.md
 create mode 100644 chef-repo/cookbooks/tomcat/attributes/default.rb
 create mode 100644 chef-repo/cookbooks/tomcat/metadata.rb
 create mode 100644 chef-repo/cookbooks/tomcat/recipes/default.rb
 create mode 100644 
chef-repo/cookbooks/tomcat/templates/default/default_tomcat6.erb
 create mode 100644 
chef-repo/cookbooks/tomcat/templates/default/server.xml.erb
 create mode 100644 
chef-repo/cookbooks/tomcat/templates/default/sysconfig_tomcat6.erb
Cookbook tomcat version 0.10.3 successfully installed
Installing java to /home/kallen/sbox/ops/chef-repo/cookbooks
Checking out the master branch.
Creating pristine copy branch chef-vendor-java
Downloading java from the cookbooks site at version 1.1.0 to 
/home/kallen/sbox/ops/chef-repo/cookbooks/java.tar.gz
Cookbook saved: /home/kallen/sbox/ops/chef-repo/cookbooks/java.tar.gz
Removing pre-existing version.
Uncompressing java version /home/kallen/sbox/ops/chef-repo/cookbooks.
removing downloaded tarball
4 files updated, committing changes
Creating tag cookbook-site-imported-java-1.1.0
Checking out the master branch.
Updating 5863ea6..b9302f4
Fast-forward
 chef-repo/cookbooks/java/attributes/default.rb     |   11 +-
 chef-repo/cookbooks/java/recipes/default.rb        |   26 +--
 .../java/templates/default/java.security.erb       |  290 
--------------------
 .../java/templates/default/profile-java-sh.erb     |    4 -
 4 files changed, 3 insertions(+), 328 deletions(-)
 delete mode 100644 
chef-repo/cookbooks/java/templates/default/java.security.erb
 delete mode 100644 
chef-repo/cookbooks/java/templates/default/profile-java-sh.erb
Cookbook java version 1.1.0 successfully installed
Installing apt to /home/kallen/sbox/ops/chef-repo/cookbooks
Checking out the master branch.
Creating pristine copy branch chef-vendor-apt
Downloading apt from the cookbooks site at version 1.2.2 to 
/home/kallen/sbox/ops/chef-repo/cookbooks/apt.tar.gz
Cookbook saved: /home/kallen/sbox/ops/chef-repo/cookbooks/apt.tar.gz
Removing pre-existing version.
Uncompressing apt version /home/kallen/sbox/ops/chef-repo/cookbooks.
removing downloaded tarball
3 files updated, committing changes
Creating tag cookbook-site-imported-apt-1.2.2
Checking out the master branch.
Updating b9302f4..a0389ef
Fast-forward
 chef-repo/cookbooks/apt/README.md          |   22 +++++++++++++---------
 chef-repo/cookbooks/apt/metadata.rb        |    2 +-
 chef-repo/cookbooks/apt/recipes/default.rb |    7 +++++++
 3 files changed, 21 insertions(+), 10 deletions(-)
Cookbook apt version 1.2.2 successfully installed
Installing jpackage to /home/kallen/sbox/ops/chef-repo/cookbooks
Checking out the master branch.
Creating pristine copy branch chef-vendor-jpackage
Downloading jpackage from the cookbooks site at version 0.10.0 to 
/home/kallen/sbox/ops/chef-repo/cookbooks/jpackage.tar.gz
Cookbook saved: /home/kallen/sbox/ops/chef-repo/cookbooks/jpackage.tar.gz
Removing pre-existing version.
Uncompressing jpackage version /home/kallen/sbox/ops/chef-repo/cookbooks.
removing downloaded tarball
1 files updated, committing changes
Creating tag cookbook-site-imported-jpackage-0.10.0
Checking out the master branch.
Updating a0389ef..cd5f894
Fast-forward
 chef-repo/cookbooks/jpackage/README.md             |   50 +++++++++++++++++
 chef-repo/cookbooks/jpackage/attributes/default.rb |   20 +++++++
 chef-repo/cookbooks/jpackage/metadata.rb           |   14 +++++
 chef-repo/cookbooks/jpackage/recipes/default.rb    |   58 
++++++++++++++++++++
 .../jpackage/templates/default/jpackage.repo.erb   |   49 +++++++++++++++++
 .../jpackage/templates/fedora/jpackage.repo.erb    |   49 +++++++++++++++++
 6 files changed, 240 insertions(+), 0 deletions(-)
 create mode 100644 chef-repo/cookbooks/jpackage/README.md
 create mode 100644 chef-repo/cookbooks/jpackage/attributes/default.rb
 create mode 100644 chef-repo/cookbooks/jpackage/metadata.rb
 create mode 100644 chef-repo/cookbooks/jpackage/recipes/default.rb
 create mode 100644 
chef-repo/cookbooks/jpackage/templates/default/jpackage.repo.erb
 create mode 100644 
chef-repo/cookbooks/jpackage/templates/fedora/jpackage.repo.erb
Cookbook jpackage version 0.10.0 successfully installed
Installing java to /home/kallen/sbox/ops/chef-repo/cookbooks
Checking out the master branch.
Pristine copy branch (chef-vendor-java) exists, switching to it.
Downloading java from the cookbooks site at version 1.1.0 to 
/home/kallen/sbox/ops/chef-repo/cookbooks/java.tar.gz
Cookbook saved: /home/kallen/sbox/ops/chef-repo/cookbooks/java.tar.gz
Removing pre-existing version.
Uncompressing java version /home/kallen/sbox/ops/chef-repo/cookbooks.
removing downloaded tarball
No changes made to java
Checking out the master branch.
Installing apt to /home/kallen/sbox/ops/chef-repo/cookbooks
Checking out the master branch.
Pristine copy branch (chef-vendor-apt) exists, switching to it.
Downloading apt from the cookbooks site at version 1.2.2 to 
/home/kallen/sbox/ops/chef-repo/cookbooks/apt.tar.gz
Cookbook saved: /home/kallen/sbox/ops/chef-repo/cookbooks/apt.tar.gz
Removing pre-existing version.
Uncompressing apt version /home/kallen/sbox/ops/chef-repo/cookbooks.
removing downloaded tarball
No changes made to apt
Checking out the master branch.

01/11 
02:
 
 git branch -a 
  chef-vendor-apt
  chef-vendor-java
  chef-vendor-jpackage
  chef-vendor-route53
  chef-vendor-s3cmd
  chef-vendor-tomcat
* master
  remotes/origin/HEAD -> origin/master
  remotes/origin/master