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This option was being applied in the wrong place - within the map layer classes themselves. This meant that depending on the user's setting for this option, a plugin calling QgsMapLayer::setName would not be guaranteed the same behaviour across installs. (and the same with setDataSource) Similarly, the option was re-applied on project load, so moving projects between installs with different values for this setting would affect the project layer names, breaking expressions which relied on these... Instead, move the formatting and capitalization of layer names to the QgisApp add*Layer methods instead, so this option only applies on adding new layers to a project.