griffon programming error: unable to find class annotation

Question 1

As you are using threading annotations you should import griffon.transform.Threading on your controller.

package test1

import griffon.util.GriffonNameUtils as GNU
import griffon.transform.Threading 

class Test1Controller {

    def model

    def clear = {
            model.griffonClass.propertyNames.each { name -> model[name] = ''
            }
    }

    @Threading(Threading.Policy.SKIP)
    def submit = {
            java.swing.JoptionPane.showMessageDialog(
            app.windowManager.windows.find{it.focused}, 
            model.griffonClass.propertyNames.collect([]) {
                     name -> "${GNU.getNaturalName(name)} = ${model[name]}"
            }.join('n')
            )
    }

}

Question 2

Application signing should happen by default. When run-webapp is invoked the signature is taken from griffon-app/conf/BuildConfig.groovy. This signature is a self-signed one when running in development. For example, the following output is form running webstart mode in development without any configuration changes

Welcome to Griffon 1.2.0 - http://griffon-framework.org/
Licensed under Apache Standard License 2.0
Griffon home is set to: /usr/local/griffon

Base Directory: /private/tmp/test1
Running script /usr/local/griffon/scripts/RunWebstart.groovy
Resolving dependencies...
Dependencies resolved in 857ms.
Environment set to development
Resolving framework plugin dependencies ...
Framework plugin dependencies resolved in 1495 ms.
Resolving plugin dependencies ...
Plugin dependencies resolved in 807 ms.
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/classes/cli
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/classes/main
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/classes/test
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/test-classes
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/test-resources
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/resources
 [griffonc] Compiling 8 source files to /Users/aalmiray/.griffon/1.2.0/projects/test1/classes/main
 [griffonc] Compiling 3 source files to /Users/aalmiray/.griffon/1.2.0/projects/test1/classes/main
    [mkdir] Created dir: /private/tmp/test1/dist/webstart
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/resources/griffon-app/i18n
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/resources/griffon-app/resources
     [copy] Copying 2 files to /Users/aalmiray/.griffon/1.2.0/projects/test1/resources/griffon-app/i18n
     [copy] Copying 8 files to /Users/aalmiray/.griffon/1.2.0/projects/test1/resources/griffon-app/resources
     [copy] Copying 1 file to /Users/aalmiray/.griffon/1.2.0/projects/test1/classes/main
     [copy] Copying 11 files to /Users/aalmiray/.griffon/1.2.0/projects/test1/resources
     [copy] Copied 8 empty directories to 8 empty directories under /Users/aalmiray/.griffon/1.2.0/projects/test1/resources
Auto-generating a local self-signed key
   [genkey] Generating Key for development
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/groovy-all-2.0.6.jar to /private/tmp/test1/staging/groovy-all-2.0.6.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/griffon-rt-1.2.0.jar to /private/tmp/test1/staging/griffon-rt-1.2.0.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/slf4j-api-1.7.2.jar to /private/tmp/test1/staging/slf4j-api-1.7.2.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/log4j-1.2.17.jar to /private/tmp/test1/staging/log4j-1.2.17.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/slf4j-log4j12-1.7.2.jar to /private/tmp/test1/staging/slf4j-log4j12-1.7.2.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/jcl-over-slf4j-1.7.2.jar to /private/tmp/test1/staging/jcl-over-slf4j-1.7.2.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/jul-to-slf4j-1.7.2.jar to /private/tmp/test1/staging/jul-to-slf4j-1.7.2.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/griffon-swing-runtime-1.2.0.jar to /private/tmp/test1/staging/griffon-swing-runtime-1.2.0.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
      [jar] Building jar: /private/tmp/test1/staging/test1.jar
   [delete] Deleting directory /Users/aalmiray/.griffon/1.2.0/projects/test1/resources/griffon-app/resources
    [mkdir] Created dir: /Users/aalmiray/.griffon/1.2.0/projects/test1/resources/griffon-app/resources
     [copy] Copying 1 file to /private/tmp/test1/staging
  [signjar] Signing JAR: /private/tmp/test1/staging/test1.jar to /private/tmp/test1/staging/test1.jar as development
  [signjar] Warning: 
  [signjar] The signer certificate will expire within six months.
  [signjar] Enter Passphrase for keystore: Enter key password for development: 
     [copy] Copying 11 files to /private/tmp/test1/staging
     [copy] Copying 18 files to /private/tmp/test1/dist/webstart
     [copy] Copied 3 empty directories to 2 empty directories under /private/tmp/test1/dist/webstart
      [zip] Building zip: /private/tmp/test1/dist/webstart/test1-0.1-webstart.zip

Couldn't fail to notice net.sourceforge.jnlp.LaunchException in the stack trace you posted. Are you using a different JNLP launcher other from the one provided by the JDK? Also, what's the output of running griffon -version? Mine is

------------------------------------------------------------
  Griffon 1.2.0
------------------------------------------------------------

   Build: 11-Jan-2013 09:10 AM
  Groovy: 2.0.6
     Ant: 1.8.4
   Slf4j: 1.7.2
  Spring: 3.2.0.RELEASE
     JVM: 1.6.0_37 (Apple Inc. 20.12-b01-434)
      OS: Mac OS X 10.7.5 x86_64