Folders missing in project pane in Webstorm

It can be caused by the corrupted .idea/modules.xml project file. You can either try to fix it manually (restore from Local History, version control or backup) or create the new project from scratch.

Check this issue for the hints/workarounds.

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It happens sometimes in WebStorm 9. The easiest way to fix it for me:

close WebStorm; in project's folder remove .idea/ (hidden directory); open your project, enjoy:)

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Solution:

Creating a new project from existing sources

File => New => Project Select "Empty Project" Browse to the location of your project with folder issues Click "Create" Select "Create from Existing Sources" in the "Directory Is Not Empty" dialog

Why this solution:

Editing and deleting in various combinations of .idea and XML files did not solve the issue for me. Hence the solution above. Back up your .idea directory in case you have project customizations you want to keep. This likely overwrites them.

Outcome:

All the various folders I had created were now visible and the project worked as expected. The .idea directory was now formatted correctly with all the necessary files.

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Find the .idea/modules.xml in your project root make sure that these lines are correct :

<modules>
  <module fileurl="file://$PROJECT_DIR$/.idea/NameOfYourProject.iml" filepath="$PROJECT_DIR$/.idea/NameOfYourProject.iml" />
</modules>

Replace NameOfYourProject.iml with the name of your project.

Then, make sure that the file .idea/NameOfYourProject.iml exists, if not , create it and put this in it :

<?xml version="1.0" encoding="UTF-8"?>
<module type="WEB_MODULE" version="4">
  <component name="NewModuleRootManager">
    <content url="file://$MODULE_DIR$" />
    <orderEntry type="inheritedJdk" />
    <orderEntry type="sourceFolder" forTests="false" />
    <orderEntry type="module-library">
      <library name="PHP">
        <CLASSES>
          <root url="file://$MODULE_DIR$/../../php/PEAR" />
        </CLASSES>
        <SOURCES />
      </library>
    </orderEntry>
  </component>
</module>

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You do not need to delete whole .idea folder and reconfigure your whole project, just

delete the .idea/modules.xml restart the IDE and your folders are there again!

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I ran into the same issue and resolved it by invalidating the cache. The option is under File > Invalidate Caches/Restart. On the prompt click Invalidate and restart.

Note: The project in concern needs to be open before you do this.

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I see this from time to time. I use Git, and I have my .gitignore file set up as recommended, specifically:

.idea/workspace.xml
.idea/tasks.xml
.idea/*.iml

I sometimes see this after cloning the repository, and when trying to figure out why, I came across this post and read the accepted answer.

I deleted the modules.xml file and reopened WebStorm (2016.2.4), and it was resolved. I looked at the new modules.xml and found that its contents were exactly the same as before, but my <projectName>.iml file was bigger.

So it seems to be a corruption in the .iml file, not modules.xml. I assume that deleting modules.xml triggers a rebuild of the .iml file. Not sure if this helps anyone with anything, but thought I would offer the extra insight.

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floor 36 solve my problem. in WebStrorm 11

It happens sometimes in WebStorm 9. The easiest way to fix it for me:

close WebStorm; in project's folder remove .idea/ (hidden directory); open your project, enjoy:)

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Try deleting workspace.xml and watchertask.xml then just restart the IDE. You must see your full source code in all folders there.

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Finally I found the culprit, it was Team Foundation Server - Version Control Integration plugin from https://plugins.jetbrains.com/plugin/7961-team-foundation-server--version-control-integration/

I looked at the system/log/idea.log file and found that this plugin was producing Null exception whenever I open a new folder as a new project and breaks the content root auto detection by the IDE, and after I uninstalled this plugin, all folders show up as it should.

You might have this issue because of a culprit plugin, and disabling those which you have just installed recently just before this issue occurs, will resolve the issue. Check the log file and search for ERROR.

If it is found to be an important plugin you are actively using which you are not willing to disable, then a temporary fix is to open Settings->Directories and click Add content root button to add the root folder of your project, click Ok now folders will show up and indexing will begin, and of course you have to do this everytime you open a new folder as new project.

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