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One of PHPEdit's guideline is to be highly customizable, this is why PHPEdit uses a complex system of settings contexts and inheritance.
Simply put, you can define different settings for different contexts: the whole application, a solution, a project, a directory in the project, etc... For each of these contexts you can store the settings in 1 to 3 different locations. For example for a project, you can specifiy that a particular setting should be stored directly in the project's .PHPEditProject file: that way, every other developper who works on the same project will benefit of the same settings. If on the contrary you don't want to share this setting, you can specify that this setting will be stored in your profile directory, and you will be the only one using this setting.
PHPEdit settings inherit from parent level settings: if you don't change a setting in a particular context, the parent context will be used to find the setting, and so on until a value is found.
For example if PHPEdit is requested to start a debug session, it will look in the active project to see if there are debugger settings. If nothing is defined in the project, the project's solution will be checked. If there's nothing in the solution either, the application settings will be checked, and on last resort the default settings.
To access to a specific item's settings, right click on the item (Solution, Project, Directory, File) in the solution explorer and click on Settings .
Automatic folders are a special case: since they are refreshed automatically depending on what's found on the disk, only the top level automatic folder can have it's own settings. So if you try to edit a child automatic folder's settings, it's in fact the top level automatic folder's settings your are editing.
See also the settings dialog for more information on editing your item's settings.
A lot of modules from the IDE store their data in the project settings, instead of the application settings. This data is loaded from the project when it's made active, and saved just before it becomes inactive. When there's no opened project, a project called DefaultProject is considered to be the active project. It is a virtual, invisible project, but still has a settings file in your profile directory, so it is able to remember your settings too.
Currently the settings that are remembered automatically are: