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I'd like to save the project-dependent configuration of my Python plugin inside the QGIS project file. Is this possible and what are best practices to do so?

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This should do it:

QgsProject.instance().writeEntry(plugin_name, property, value)

Then you just need to save the project.

Reading is performed with one of the following functions:

readEntry (plugin_name, property)
readNumEntry (plugin_name, property)
readDoubleEntry (plugin_name, property)
readBoolEntry (plugin_name, property)

Doc: http://qgis.org/api/classQgsProject.html

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