Phpstorm 2017.3 inspections not refresh after context changed
Inspections highlight errors, and not refresh highlighting when errors has been fixed;
After restarting phpstorm, the existed code haven't wrong highlights, but this behavior repeat again during working process
I tried to clean cache and restart, but it doesn't help
So in this screen defined variables highlighted as undefined

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I have similar issue. After upgrade to 2017.3 I have major problems with inspections and code coloring. Phpstorm seems to not recognize variables and context properly. I restarted & cleared cache many times. It 'refreshes' current broken state only, but new bugs keep occurring. It seems to 'cache' variables before end of typing and keep track invalid partial name. See attached screenshot.

Most probably the problem was 'Php Inspections (EA Extended)' plugin. Disabling it seems to fix my issue for now.
Thanks, solved after upgrade Yii2-inspections plugin.
I also have an issue with refreshing the codebase, for example when I commit my code via console, the status of the file is not updated and remains in the status 'changed'.
After refreshing the project tree manually, the change is detected and the status changes to 'unchanged'
Also when code changes outside of the IDE, these changes are not applied in the IDE, for example when switching branches. Only when manually refreshing the project tree yet again, the changes become visible.
This is highly annoying
PhpStorm 2017.3.1 EAP
Build #PS-173.3942.13, built on December 6, 2017
JRE: 1.8.0_152-release-1024-b8 amd64
JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o
Windows 10 10.0
Both issues have the same cause, please vote here https://youtrack.jetbrains.com/issue/IDEA-12116
Link is dead. Can you provide the correct one?
Sorry, failed to paste properly https://youtrack.jetbrains.com/issue/IDEA-121164