Currently we do not plan to integrate PyLint and PyFlakes. PyCharm covers all the features of PyFlakes and a lot of features of PyLint. In PyCharm 3.0 we will add more PyLint-like inspections, see our development roadmap.
"PyCharm covers all the features of PyFlakes and a lot of features of PyLint"

Where can I find information on how to configure these features on per file/scope/line basis (comments in the source code) similarly to how the original tools can be configured?
Inspections are configured in File | Settings | Inspections, see Code Inspection. You can suppress inspection warnings using the quick fix menu on the highlighted code, see Suppressing Inspections.
The problem with this is that organizations can extend pylint, which gives it value. Even if we could add pycharm-specific inspections, I'd fight against it as I don't like to invest in closed-source-specific solutions. :-(
PyCharm Community Edition, that includes most inspections and refactorings is in fact open-source. We may consider adding a generic mechanism for adding custom code inspections as we did for pep8.
Here is my use case. I do lot of coding in PyCharm, sometimes i have to fix issues and do things in random text editors, including nano. Our code goes through continuous integration servers, and we run flake8 on the servers. Flake8 currently flags a ton of stuff that Pycharm doesnt flag by default (W293, W291, E501 etc) , hence, i'd like to have an easy option of running flake8 ( as well as pycharms own live-checking ) from within the IDE so i dont have to roundtrip through buildservers, jump to commandline etc to do this.

Someone keeps a gist sort of up to date here for this : https://gist.github.com/jsmits/9033655

I don't understand at all. There is a well-known community tool `flake8`, free, open-source, and available through pypi/pip. A lot of projects use this tool in their CI systems. Why pycharm-flake8 plugin still does not exist??? 

Moreover, as written before, PyCharm's embed linting feature does not detect a lot of bugs/issues/tips, already detected by flake8.

I know just one so-so way to use flake8 in PyCharm: use External Tools. There is an article: https://foxmask.trigger-happy.eu/post/2016/02/17/pycharm-running-flake8/ , and here is my config:



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