I am using Intellij IDEA 12.1.6. Some of the top level or functional files names are in brick red text. For example, the manifest file and the .iml file. I am concerned about the iml file, because that is the project file.
IDEA documentation says that it "highlights" text in red if there is a merge conflict in the file, however, when I open the iml file, there is no merge conflict in it. Also, the text is in red, it is not highlighted, although it is possible that by "highlighted" they mean the color of the text.
Why would the text of the file name be in red? Screenshot is below:
It means that the files exist locally, but are not in the repository, and are not scheduled for addition. With other words, the files are not under version control. There is not really a problem since the files can just be added to the VCS if desired.
It means Excluded Root and is explained in IntelliJ IDEA Docs as: Excluded roots are ones that IntelliJ IDEA "partially ignores".
IDEA documentation says that it "highlights" text in red if there is a merge conflict in the file, however, when I open the iml file, there is no merge conflict in it. Also, the text is in red, it is not highlighted, although it is possible that by "highlighted" they mean the color of the text.
Orange is the color for excluded folders. IntelliJ excludes indirect dependencies automatically as you shouldn't be importing those. Also, having the indirect dependencies excluded also speeds up the search.
A merge conflict is actually a bright red. What you have there is "brown" and indicates the file is not known to version control. You can see the colors used in the Help at References > Version Control Reference > File status highlights or on the web at http://www.jetbrains.com/idea/webhelp/file-status-highlights.html
You can either add those files to VCS, or ignore them. If you open the changes tool window, you will have a list of unknown files. Those files will be in that list.
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