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According to this question, I can use Java System Property in tomcat's conf xml. Does this also apply to hadoop's configuration file, like core-site.xml, hdfs-site.xml? Thank you!

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Yes, you can. e.g.

<property>
    <name>dfs.name.dir</name>
    <value>${user.home}/hadoop-1.2.1/hdfs/name</value>
</property>
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