It's recommended to create the 'Home' directory separately from the 'Install' directory, however if you've already combined the two directories this will help you untangle them...
1. Stop Confluence
2. Backup your current home/installation directory
3. Create a new blank home directory (parent only, no sub-directories)
4. Move the following files/directories to the new home directory
- attachments
- backups
- bundled-plugins
- bundled-plugins_language
- config
- confluence.cfg.xml
- index
- plugin-cache
- plugins-osgi-cache
- plugins-temp
- viewfile
5. There are two sub-directories which will need to be created in the home directory:
- logs
It's fine to leave this empty, however if you want to keep your existing confluence log move the atlassian-confluence.log file from the existing 'logs' directory to the newly created one
- temp
This is also fine to leave empty
6. Edit the confluence/WEB-INF/classes/confluence-init.properties file to reflect the new home directory path (the one created in Step 3)
7. Start Confluence
Did it work?
If you've followed the steps correctly, your new installation and home directories should look like this:
Home
Install
You should have no problems starting Confluence, and the log files should be updated as normal.
If Confluence tries to load a new site (such as in a new installation) you'll need to confirm that the home directory path is specified correctly in confluence-init.properties.
If you find you're unable to search or the recently updated menu isn't showing any content try rebuilding your search index via Confluence Admin > Content Indexing