I have two standalone modules that use Camel's Main. Both of them contain:
main.setPropertyPlaceholderLocations( "classpath:application.properties" );
and I also tried:
main.setPropertyPlaceholderLocations( "application.properties" );
If I run them from within Eclipse both work fine (having added <project>/target to the Run Configurations' Classpath).
If I run them from the cmd line:
...\target> java -jar <module>.jar
with target containing both application.properties and <module>.jar, one works fine. The other results in:
Exception in thread "main" org.apache.camel.RuntimeCamelException: java.io.FileNotFoundException:
Properties file application.properties not found in classpath
I've seen Q: Camel properties file not found in class path but my application.properties is in src/main/resources, and copied to target during mvn package.
UPDATE 1
For clarification. In my projects' POMs I use:
    <resources>
        <resource>
            <directory>src/main/resources</directory>
            <excludes>
                <exclude>application.properties</exclude>
            </excludes>
        </resource>
        <resource>
            <directory>src/main/resources</directory>
            <includes>
                <include>application.properties</include>
            </includes>
            <targetPath>..</targetPath>  <!-- relative to target/classes -->
        </resource>
    <resources>
to prevent application.properties residing inside <module>.jar.
UPDATE 2
90   [main] INFO  <module>  - Starting Camel...
182  [main] INFO  org.apache.camel.impl.DefaultCamelContext  - Apache Camel 2.22.0 (CamelContext: camel-1) is shutting down
195  [main] INFO  org.apache.camel.impl.DefaultCamelContext  - Apache Camel 2.22.0 (CamelContext: camel-1) uptime
198  [main] INFO  org.apache.camel.impl.DefaultCamelContext  - Apache Camel 2.22.0 (CamelContext: camel-1) is shutdown in 0.017 seconds
Exception in thread "main" org.apache.camel.RuntimeCamelException: java.io.FileNotFoundException: Properties file application.properties not found in classpath
        at org.apache.camel.util.ObjectHelper.wrapRuntimeCamelException(ObjectHelper.java:1830)
        at org.apache.camel.model.RouteDefinitionHelper.initRouteInputs(RouteDefinitionHelper.java:382)
        at org.apache.camel.model.RouteDefinitionHelper.prepareRouteImp(RouteDefinitionHelper.java:298)
        at org.apache.camel.model.RouteDefinitionHelper.prepareRoute(RouteDefinitionHelper.java:270)
        at org.apache.camel.model.RoutesDefinition.route(RoutesDefinition.java:205)
        at org.apache.camel.model.RoutesDefinition.from(RoutesDefinition.java:158)
        at org.apache.camel.builder.RouteBuilder.from(RouteBuilder.java:169)
        at <module>Route.configure(<module>Route.java:24)
        at org.apache.camel.builder.RouteBuilder.checkInitialized(RouteBuilder.java:462)
        at org.apache.camel.builder.RouteBuilder.configureRoutes(RouteBuilder.java:402)
        at org.apache.camel.builder.RouteBuilder.addRoutesToCamelContext(RouteBuilder.java:383)
        at org.apache.camel.impl.DefaultCamelContext$1.call(DefaultCamelContext.java:1029)
        at org.apache.camel.impl.DefaultCamelContext$1.call(DefaultCamelContext.java:1026)
        at org.apache.camel.impl.DefaultCamelContext.doWithDefinedClassLoader(DefaultCamelContext.java:3272)
        at org.apache.camel.impl.DefaultCamelContext.addRoutes(DefaultCamelContext.java:1026)
        at org.apache.camel.main.MainSupport.postProcessCamelContext(MainSupport.java:612)
        at org.apache.camel.main.MainSupport.postProcessContext(MainSupport.java:550)
        at org.apache.camel.main.Main.doStart(Main.java:136)
        at org.apache.camel.support.ServiceSupport.start(ServiceSupport.java:61)
        at org.apache.camel.main.MainSupport.run(MainSupport.java:170)
        at <module>.run(<module>.java:44)
        at <module>.main(<module>.java:20)
Caused by: java.io.FileNotFoundException: Properties file application.properties not found in classpath
        at org.apache.camel.component.properties.DefaultPropertiesResolver.loadPropertiesFromClasspath(DefaultPropertiesResolver.java:112)
        at org.apache.camel.component.properties.DefaultPropertiesResolver.resolveProperties(DefaultPropertiesResolver.java:69)
        at org.apache.camel.component.properties.PropertiesComponent.parseUri(PropertiesComponent.java:207)
        at org.apache.camel.component.properties.PropertiesComponent.parseUri(PropertiesComponent.java:178)
        at org.apache.camel.impl.DefaultCamelContext.resolvePropertyPlaceholders(DefaultCamelContext.java:2552)
        at org.apache.camel.model.ProcessorDefinitionHelper.resolvePropertyPlaceholders(ProcessorDefinitionHelper.java:735)
        at org.apache.camel.model.RouteDefinitionHelper.initRouteInputs(RouteDefinitionHelper.java:380)
        ... 20 more
204  [Camel Thread #0 - CamelHangupInterceptor] INFO  org.apache.camel.main.MainSupport$HangupInterceptor  - Received hang up - stopping the main instance.