I tried digging into this a bit and ran out of time, so I thought it was best to open an issue even though I didn't find the fix. I see that a search path is set for jinja2, but I can't figure out why it is seemingly not being searched...

I can confirm the bug being present in latest Ansible 2.0 beta release. Here's an example test case which errors on Ansible 2.0 but works fine on Ansible 1.9.2.

Ahh, tracked this down to the fix merged in in #9933, which incorrectly set the value on the self._templar.environment.searchpath instead of self._templar.environment.loader.searchpath. After correctly assigning the value there, the example provided by @drybjed works without error:

# ansible-playbook -vv site.yml 
Using /etc/ansible/ansible.cfg as config file
1 plays in site.yml
PLAY ***************************************************************************
TASK [ansible-template-test : Generate the file from templates] ****************
changed: [localhost] => {"changed": true, "checksum": "94dec40f15539fd4777b885cbe4423a4b78fb5a7", "dest": "/tmp/output-file", "gid": 0, "group": "root", "md5sum": "0bdd04bb72f25fab6582d6079a0ff9a7", "mode": "0644", "owner": "root", "secontext": "unconfined_u:object_r:user_tmp_t:s0", "size": 91, "src": "/root/.ansible/tmp/ansible-tmp-1441143378.51-9017626803498/source", "state": "file", "uid": 0}
PLAY RECAP *********************************************************************
localhost                  : ok=1    changed=1    unreachable=0    failed=0   
# cat /tmp/output-file 
# This file is managed by Ansible, all changes will be lost
First example
Second example

We believe the above commit should resolve this problem for you. This will also be included in the next major release.

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Thank you!

Fix confirmed over here as well. Thanks @jimi-c!