I had a similar problem until I made my nutch-site.xml look like this
<?xml version="1.0"?>
<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
<!-- Put site-specific property overrides in this file. -->
<configuration>
<property>
<name>http.agent.name</name>
<value>testing</value>
<description></description>
</property>
<property>
<name>http.agent.description</name>
<value>testing the nutch bot</value>
<description></description>
</property>
<property>
<name>http.agent.url</name>
<value></value>
<description>none</description>
</property>
<property>
<name>http.agent.email</name>
<value>none</value>
<description></description>
</property>
<property>
<name>plugin.includes</name>
<value>protocol-file|protocol-http|parse-(text|html|js)|index-basic|query-(basic|site|url)|summary-basic|scoring-opic</value>
</property>
<property>
<name>file.content.limit</name>
<value>-1</value>
</property>
</configuration>
hope this helps, and if you can get nutch to index a file system please let
me know hor you did it.
jim s