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This is necessary in order to be able to correctly translate between absolute and relative paths deeper in the code - e.g. paths to SVG files used in marker or fill symbols. Until now, relative paths were translated to absolute paths on the fly. This is now changed - paths to files should be always absolute within QGIS objects - and paths only get turned into relative when saving projects. When loading a project, relative paths are translated to absolute paths immediately. This should lower the overall confusion about relative/absolute paths within QGIS, and also allow having different base directories for relative paths (e.g. QML or QPT files may use relative paths to their directory - rather than to the project directory)