Whether done manually or with the GUI, the HTMLConverter will not convert subdirectories. Any html files that are in sub directories result in an exception. The following example is an execution of the HTMLConverter where there is a subdirectory called bill, with a file index.html in it:

tirpitz 161 =>java -jar htmlconv1_3.jar
java.io.FileNotFoundException: index.html (No such file or directory)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:64)
        at java.io.FileInputStream.<init>(FileInputStream.java:95)
        at java.io.FileReader.<init>(FileReader.java:50)
        at sun.plugin.converter.util.StdUtils.countWords(StdUtils.java:97)
        at sun.plugin.converter.engine.PluginConverter.runConversion(PluginConverter.java:314)
        at sun.plugin.converter.engine.PluginConverter.runConversion(PluginConverter.java:293)
        at sun.plugin.converter.engine.PluginConverter.run(PluginConverter.java:250)
        at java.lang.Thread.run(Thread.java:484)

Also, if there are two files and they are both called index.html, one in the subdirectory bill and the other in the current directory, the HTMLConverter will convert the one in the current directory and leave the one in the subdirectory unmodified. The convertlog.txt gives the following message:

Applet Conversion September 16, 2000 5:39:58 PM EDT
/home/billyh/plugin/index.html Processing...Done Applets Found: 1
bill/index.html Processing...File previously converted, no conversion is necessary. Done Applets Found: 0
All Done Files Processed: 2 Applets Found: 1