When things are remapped by the Symbian Source File Remapping only capture the directory the file was discovered in, not the entire drive.
bin.includes = .,\
META-INF/,\
icons/,\
plugin.xml,\
html/,\
Tools/,\
tocCodeScanner.xml,\
book.css,\
CodeScannerPlugin.jar,\
index/
jars.compile.order = CodeScannerPlugin.jar
source.CodeScannerPlugin.jar = src/
output.CodeScannerPlugin.jar = bin/