1)
There seem to be 2 different catalina.properties:

jakarta-tomcat-5.0.16-src\jakarta-tomcat-catalina\catalina\src\conf\cata
lina.properties
shared.loader=${catalina.base}/shared/classes,${catalina.base}/shared/li
b/*.jar
        - this winds up in CATALINA_HOME/conf, but when the binary
tarball is expanded, the permissions are 600.  So, in my case the file
does not get read

jakarta-tomcat-5.0.16-src\jakarta-tomcat-catalina\catalina\src\share\org
\apache\catalina\startup\catalina.properties
shared.loader=${catalina.home}/shared/classes,${catalina.home}/shared/li
b/*.jar
        - this winds up inside bootstrap.jar.  Note this version says
catalina.home, instead of catalina.base.

According to
http://jakarta.apache.org/tomcat/tomcat-5.0-doc/class-loader-howto.html
the second file is incorrect.

        If multiple Tomcat instances are run from the same binary using
the $CATALINA_BASE environment variable, then   this classloader
repositories are relative to $CATALINA_BASE rather than $CATALINA_HOME. 

2) 
By default, org/apache/catalina/startup/CatalinaProperties.java looks
for catalina.properties in CATALINA_HOME.  Since the user might want to
customize a CATALINA_BASE directory, shouldn't it look in CATALINA_BASE?

3)
According to org/apache/catalina/startup/CatalinaProperties.java, the
location of catalina.properties can be specified via the catalina.config
option.  Shouldn't that be documented in the catalina.properties file?

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