WIKINDX will not function correctly if various folders and files are not writeable by the web server user. The following, shown with their current permissions, should be made writeable:
attachments: 0750
templates/default: 0750
templates/default/description.txt: 0640
templates/compiled_templates: 0750
templates/bryophyta: 0750
templates/bryophyta/description.txt: 0640
templates/IFE: 0750
templates/IFE/description.txt: 0640
templates/verticalOrange: 0750
templates/verticalOrange/description.txt: 0640
templates/simpleBlue: 0750
templates/simpleBlue/description.txt: 0640
templates/enluminure: 0750
templates/enluminure/description.txt: 0640
plugins/adminstyle: 0750
plugins/adminstyle/config.php: 0750
plugins/adminstyle/index.php: 0750
plugins/userwritecategory: 0750
plugins/userwritecategory/config.php: 0750
plugins/userwritecategory/index.php: 0750
plugins/importamazon: 0750
plugins/importamazon/config.php: 0750
plugins/importamazon/index.php: 0750
plugins/test: 0750
plugins/test/config.php: 0750
plugins/test/index.php~: 0750
plugins/chooseLanguage: 0750
plugins/chooseLanguage/config.php: 0750
plugins/chooseLanguage/index.php: 0750
plugins/wordProcessor: 0750
plugins/wordProcessor/config.php: 0750
plugins/wordProcessor/index.php: 0750
plugins/inline1: 0750
plugins/inline1/config.php: 0750
plugins/inline1/index.php~: 0750
plugins/importexportbib: 0750
plugins/importexportbib/config.php: 0750
plugins/importexportbib/index.php: 0750
plugins/localization: 0750
plugins/localization/config.php: 0750
plugins/localization/index.php~: 0750
styles/bibliography: 0750
styles/bibliography/chicago/CHICAGO.xml: 0640
styles/bibliography/wikindx/WIKINDX.xml: 0640
styles/bibliography/ieee/IEEE.xml: 0640
styles/bibliography/turabian/TURABIAN.xml: 0640
styles/bibliography/vste/VSTE.xml: 0640
styles/bibliography/mla/MLA.xml: 0640
styles/bibliography/copie-style-vst/COPIE-STYLE-VST.xml: 0640
styles/bibliography/britishmedicaljournal/BRITISHMEDICALJOURNAL.xml: 0640
styles/bibliography/harvard/HARVARD.xml: 0640
styles/bibliography/apa/APA.xml: 0640
styles/bibliography/vst/VST.xml: 0640
styles/CACHE: 0750
languages: 0750
languages/reference/ERRORS.php: 0640
languages/reference/CONSTANTS.php: 0640
languages/reference/MESSAGES.php: 0640
languages/reference/SUCCESS.php: 0640
languages/reference/HELP.php: 0640