think you can do whatever you like with your own repo, but the question is 
ambigitous.
web2py in terms of web2py root folder that contain 
-rw-rw-r--   1 tetsu  staff   66446 Aug  6 08:02 CHANGELOG
-rw-rw-r--   1 tetsu  staff    5727 Aug  6 08:02 LICENSE
-rw-rw-r--   1 tetsu  staff      24 Aug  6 08:02 MANIFEST.in
-rw-rw-r--   1 tetsu  staff    3896 Aug  6 08:02 README.markdown
-rw-rw-r--   1 tetsu  staff      52 Aug  6 08:02 VERSION
-rw-rw-r--   1 tetsu  staff   12960 Aug  6 08:02 anyserver.py
drwxr-xr-x   8 tetsu  staff     272 Aug  7 11:30 applications
drwxr-xr-x   2 tetsu  staff      68 Aug  7 11:30 deposit
drwxr-xr-x  11 tetsu  staff     374 Aug  6 09:39 examples
drwxr-xr-x   4 tetsu  staff     136 Aug  6 09:38 extras
-rw-rw-r--   1 tetsu  staff    6091 Aug  6 08:02 fabfile.py
drwxr-xr-x  88 tetsu  staff    2992 Sep  3 09:27 gluon
drwxr-xr-x  11 tetsu  staff     374 Aug  6 09:39 handlers
drwxr-xr-x   2 tetsu  staff      68 Aug  7 11:30 logs
drwxr-xr-x  46 tetsu  staff    1564 Aug  6 09:39 scripts
drwxr-xr-x   3 tetsu  staff     102 Aug  6 09:39 site-packages
-rwxrwxr-x   1 tetsu  staff     900 Aug  6 08:02 web2py.py
-rw-r--r--   1 tetsu  staff  419727 Aug  7 11:30 welcome.w2p

or web2py app e.g. welcome
-rw-rw-r--   1 tetsu  staff    55 Aug  6 08:02 ABOUT
-rw-rw-r--   1 tetsu  staff   208 Aug  6 08:02 LICENSE
-rw-rw-r--   1 tetsu  staff     1 Aug  6 08:02 __init__.py
drwxrwxr-x   4 tetsu  staff   136 Aug  6 08:02 controllers
drwxrwxr-x   4 tetsu  staff   136 Aug  6 08:02 cron
drwxr-xr-x  10 tetsu  staff   340 Aug  7 11:44 databases
drwxr-xr-x   2 tetsu  staff    68 Aug  7 11:44 errors
drwxrwxr-x  33 tetsu  staff  1122 Aug  6 08:02 languages
drwxrwxr-x   4 tetsu  staff   136 Aug  6 08:02 models
drwxrwxr-x   4 tetsu  staff   136 Aug  7 21:32 modules
drwxrwxr-x   3 tetsu  staff   102 Aug  6 08:02 private
-rw-rw-r--   1 tetsu  staff  2354 Aug  6 08:02 routes.example.py
drwxr-xr-x   2 tetsu  staff    68 Aug  7 11:44 sessions
drwxrwxr-x   9 tetsu  staff   306 Aug  6 08:02 static
drwxr-xr-x   2 tetsu  staff    68 Aug  7 11:44 uploads
drwxrwxr-x  16 tetsu  staff   544 Aug  6 08:02 views

just a suggestion better to maintain your web2py app in your repo, not the 
web2py itself, except you want fix some bug or add some feature in web2py, 
but again better to separate it.
for integrate with jenkins after you commit it (svn or git) and trigger to 
update the web2py app, think you can achieve it, but pls look in jenkins 
website or ask in their forum about how to do it.

best regards,
stifan

-- 
Resources:
- http://web2py.com
- http://web2py.com/book (Documentation)
- http://github.com/web2py/web2py (Source code)
- https://code.google.com/p/web2py/issues/list (Report Issues)
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