void saveProject() {
		Project project = plugin.getActiveProject();
		if (project == null) {
			return;
		}

		if (!project.saveSessionTools()) {
			// if tools have conflicting options, user is presented with a dialog that can
			// be cancelled. If they press the cancel button, abort the entire save project action.
			return;
		}

		doSaveProject(project);
		Msg.info(this, "Saved project: " + project.getName());
	}
menu listener for File | Save Project
Ghidra/Framework/Project/src/main/java/ghidra/framework/main/FileActionManager.java