Hi Risto,
The error occurs for all those directories, and not just classpath. Classpath is the higher priority for me, however.
permissions on bin/ is drwxr-xr-x, bin/main/ is drwxrwxrwx. assets does not work either, but perms there are drwxr-xr-x.
here is an excerpt from the jrebel log, set to debug or trace, I believe:
2016-10-31 14:00:16.981 INFO [16] [Core] rebel.xml contents for '1c536c2c6bf60000857304cbc88ea697b976aaea': <?xml version="1.0" encoding="UTF-8"?>
<application generated-by="eclipse" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.zeroturnaround.com" xsi:schemaLocation="http://www.zeroturnaround.com http://update.zeroturnaround.com/jrebel/rebel-2_1.xsd">
<classpath>
<dir name="/home/jsteege/dev/cc/conference-center/bin/main">
</dir>
</classpath>
<web>
<link target="/">
<dir name="/home/jsteege/dev/cc/conference-center/src/main/webapp">
</dir>
</link>
<link target="/assets">
<dir name="/home/jsteege/dev/cc/conference-center/build/assets">
</dir>
</link>
</web>
</application>
2016-10-31 14:00:16.983 WARN [16] [Core] Invalid 'dir' defined in class path of rebel.xml (jndi:/tomcat-host-0/cc/WEB-INF/classes/rebel.xml): Directory '/home/jsteege/dev/cc/conference-center/bin/main' does not exist
2016-10-31 14:00:16.983 DEBUG [16] [IDENotifications] Sending IDE notification to http://localhost:17434: [WARN] Invalid rebel.xml, Invalid 'dir' defined in class path of rebel.xml (jndi:/tomcat-host-0/cc/WEB-INF/classes/rebel.xml): Directory '/home/jsteege/dev/cc/conference-center/bin/main' does not exist
2016-10-31 14:00:16.984 DEBUG [16] [Al] Get connection for route HttpRoute[{}->http://localhost:17434]
2016-10-31 14:00:16.984 DEBUG [16] [Ae] Connecting to localhost:17434
2016-10-31 14:00:16.984 DEBUG [16] [xI] CookieSpec selected: best-match
2016-10-31 14:00:16.984 DEBUG [16] [xJ] Auth cache not set in the context
2016-10-31 14:00:16.984 DEBUG [16] [GJ] Attempt 1 to execute request
2016-10-31 14:00:16.984 DEBUG [16] [Ad] Sending request: POST / HTTP/1.1
2016-10-31 14:00:16.984 DEBUG [16] [Ad] Receiving response: HTTP/1.1 200 OK
2016-10-31 14:00:16.985 DEBUG [16] [Al] Releasing connection com.zeroturnaround.javarebel.An@be4da0
2016-10-31 14:00:16.985 DEBUG [16] [Al] Released connection open but not reusable.
2016-10-31 14:00:16.985 DEBUG [16] [Ad] Connection shut down
2016-10-31 14:00:16.985 WARN [16] [Core] Invalid 'dir' defined in web link of rebel.xml (jndi:/tomcat-host-0/cc/WEB-INF/classes/rebel.xml): Directory '/home/jsteege/dev/cc/conference-center/src/main/webapp' does not exist
2016-10-31 14:00:16.985 DEBUG [16] [IDENotifications] Sending IDE notification to http://localhost:17434: [WARN] Invalid rebel.xml, Invalid 'dir' defined in web link of rebel.xml (jndi:/tomcat-host-0/cc/WEB-INF/classes/rebel.xml): Directory '/home/jsteege/dev/cc/conference-center/src/main/webapp' does not exist
2016-10-31 14:00:16.986 DEBUG [16] [Al] Get connection for route HttpRoute[{}->http://localhost:17434]
2016-10-31 14:00:16.986 DEBUG [16] [Ae] Connecting to localhost:17434
2016-10-31 14:00:16.986 DEBUG [16] [xI] CookieSpec selected: best-match
2016-10-31 14:00:16.986 DEBUG [16] [xJ] Auth cache not set in the context
2016-10-31 14:00:16.986 DEBUG [16] [GJ] Attempt 1 to execute request
2016-10-31 14:00:16.986 DEBUG [16] [Ad] Sending request: POST / HTTP/1.1
2016-10-31 14:00:16.986 DEBUG [16] [Ad] Receiving response: HTTP/1.1 200 OK
2016-10-31 14:00:16.986 DEBUG [16] [Al] Releasing connection com.zeroturnaround.javarebel.An@34965bd5
2016-10-31 14:00:16.986 DEBUG [16] [Al] Released connection open but not reusable.
2016-10-31 14:00:16.987 DEBUG [16] [Ad] Connection shut down
2016-10-31 14:00:16.987 WARN [16] [Core] Invalid 'dir' defined in web link of rebel.xml (jndi:/tomcat-host-0/cc/WEB-INF/classes/rebel.xml): Directory '/home/jsteege/dev/cc/conference-center/build/assets' does not exist
2016-10-31 14:00:16.987 DEBUG [16] [IDENotifications] Sending IDE notification to http://localhost:17434: [WARN] Invalid rebel.xml, Invalid 'dir' defined in web link of rebel.xml (jndi:/tomcat-host-0/cc/WEB-INF/classes/rebel.xml): Directory '/home/jsteege/dev/cc/conference-center/build/assets' does not exist
2016-10-31 14:00:16.987 DEBUG [16] [Al] Get connection for route HttpRoute[{}->http://localhost:17434]
2016-10-31 14:00:16.987 DEBUG [16] [Ae] Connecting to localhost:17434
2016-10-31 14:00:16.987 DEBUG [16] [xI] CookieSpec selected: best-match
2016-10-31 14:00:16.987 DEBUG [16] [xJ] Auth cache not set in the context
2016-10-31 14:00:16.987 DEBUG [16] [GJ] Attempt 1 to execute request
2016-10-31 14:00:16.987 DEBUG [16] [Ad] Sending request: POST / HTTP/1.1
2016-10-31 14:00:16.988 DEBUG [16] [Ad] Receiving response: HTTP/1.1 200 OK
2016-10-31 14:00:16.988 DEBUG [16] [Al] Releasing connection com.zeroturnaround.javarebel.An@7b6717eb
2016-10-31 14:00:16.988 DEBUG [16] [Al] Released connection open but not reusable.
2016-10-31 14:00:16.988 DEBUG [16] [Ad] Connection shut down