When using the configuration form for Plugin Installation in pre-6.1 GA2 or with the new plugin (http://www.liferay.com/marketplace/-/mp/application/15474932 - this form: http://www.liferay.com/marketplace?p_p_id=7_WAR_osbportlet&p_p_lifecycle=2&p_p_state=normal&p_p_mode=view&p_p_resource_id=serveMedia&p_p_cacheability=cacheLevelPage&p_p_col_id=column-2&p_p_col_count=1&_7_WAR_osbportlet_assetAttachmentId=15997508) it will write the new auto deploy directory to the database even if it's not changed directly but sent with the form. When updating the portal to a new version and changing the path of the portal (e.g. from LF6.1.0/ to LF6.1.1), the auto.deploy.deploy.dir will be shown correct in the Portal UI but it will try to deploy from the old directory.
1. Install LF 6.1 GA1 or LF 6.1 GA2 with the above linked plugin to the folder /Liferay6.1_1/
2. Go to the control panel > Plugin Installation > (Private) Plugin Installer > Configuration
3. Send the form without changing the deploy path
4. Update LF from GA1 to GA2 and move it to /Liferay6.1_2/ or just move your GA2 installation to the new folder /Liferay6.1_2/
5. Copy your data/ folder and your portal-ext.properties from the old to the new directory
6. Update liferay.home directory in your portal-ext.properties to the new folder
7. Start your portal from the new directory
8. Go to the control panel > Administration > Properties > Portal Properties and check auto.deploy.deploy.dir (it will show the new path)
9. Use any WAR and copy it to the deploy folder of the new installation in /Liferay6.1_2/deploy/ (it will not deploy)
10. Use the same WAR and copy it to the old deploy folder in /Liferay6.1_1/deploy/ (it will deploy to the new portal)
When sending the form (step 3) it will write the path to the DB in table "portalpreferences" and column "preferences" in the row with "ownerid" = 0 and "ownertype" = 1. If you change the path here, it will work correct again.
Liferay should either check the DB for this location and update the path or check if the deploy directory has changed in the form from what is in auto.deploy.deploy.dir and if it hasn't changed then don't touch the DB.