Prevent document reload with old content

[MikhailArkhipov]

Fixes #1543
Sligtly different from #1585.

Found another case of buffer corruption. Happens when module reload comes during analysis.
Repro:

• Remove black formatter if you have one installed.
• Open scikit-learn
• Open conftest.py
• While analysis is running, make changes like add space after dot in del sys._is_pytest_session
• Format document
• When prompted to install black say yes.
• When formatter is installed and analysis still running, format document.
• The buffer is now corrupted since changes comes over content reloaded by ReloadAll.

Separated Reset into SetContent, MarkChanged and Clear.
Added exceptions to make sure Populate only happens once and there is no Update after Clear.
MarkChanged advances version so analysis thinks buffer has changed without actually reloading it.