Semantic MediaWiki
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The commands which finally worked for running the SMW setup file:
cd ~/AppDev/L48/issuepedia.org/maintenance
php -r "putenv('MW_INSTALL_PATH=/home/woozle/AppDev/L48/issuepedia.org'); require('/home/woozle/AppDev/L48/issuepedia.org/extensions/smw/SemanticMediaWiki/maintenance/SMW_setup.php');"
However, it turns out to be a bad idea to put SMW in a sub-folder (extensions/smw/SemanticMediaWiki) because the extension is hard-coded to look for CSS and Java files in "extensions/SemanticMediaWiki/..." Maybe they will fix this in a later version.