When I run my script, I get this output:
/app/venv/lib/python2.7/site-packages/flask/exthook.py:71: ExtDeprecationWarning: Importing flask.ext.sqlalchemy is
I cannot decide for sure from your question, but I'm pretty sure it's the imports within your source files that're causing these warnings.
If you are using the deprecated flask.ext import redirect, then for example:
flask.ext.sqlalchemy import SQLAlchemy()
Becomes a direct import:
from flask_sqlalchemy import SQLAlchemy()
If you're using Linux, this one-liner will make the change in all your files and folders recursively (from ./).
Back up first to a different file path - I cannot say with certainty it will not corrupt the contents of a .git directory, or other svn you use, etc. Or just make the amendments manually.
find ./ -type f exec sed -i 's/flask.ext./flask_/g' {} \;