Looking For Guidance: Best Practices for Source Control of Database Assets

Database Version: 11.2.0.3
OS: RHEL 6.2
Source Control: subversion
This is a general question aimed at database professionals, however, it is not specific to any oracle version, etc.  Its a leadership question for other Oracle shops regarding source control.
The current trunk, in my client's source control, is the implementation of a previous employee who used ER Studio.  After walking the batch scripts and subordinate files , it was determined that there would be no formal or elegant way to recreate the current version of the database from our source control - the engineers who have contributed to these assets are no longer employed or available for consulting.  The batch scripts are stale, if you will.
To clean this up and to leverage best practices, I need some guidance on whether or not to baseline the current repository and how to move forward with additions of assets; tables, procs, pkgs, etc.  I'm really interested in how larger oracle shops organize their repository - what directories do you use, how are they labeled...are they labeled with respect to version?
Assumptions:
1. repository (database assets only) needs to be baselined (?)
2. I have approval to change this database directory under the trunk to support best practices and get the client steered straight in terms of recovery and
Knowns:
1. the current application version in the database is 5.11.0 (that's my client's application version)
2. this is for one schema/user of a database (other schemas under the database belong to different trunks)
This is the layout that we currently have and for the privacy of the
client I've made this rather generic.  I'd love to have a fresh
start...how do I go about doing that...initially, I like using
SqlDeveloper's ability to create sql scripts from a connected target. 
product_name
  |_trunk
     |_database
       |_config
       |_data
       |_database
       |_integration
       |_patch
       |   |_5.2A.2
       |   |_5.2A.4
       |   |_5.3.0
       |   |_5.3.1
       |
       |_scripts
       |   |_config
       |   |_logs
       |
       |_server
Thank you in advance.

HiWe are using Data ONTAP 8.2.3p3 on our FAS8020 in 7-mode and we have 2 aggregates, a SATA and SAS aggregate. I want to decommission the SATA aggregate as I want to move that tray to another site. If I have a flexvol containing 3 qtrees CIFS shares can I use data motion (vol copy) to move the flex vol on the same controller but to a different aggregate without major downtime? I know this article is old and it says here that CIFS are not supported however I am reading mix message that on the version of data ONTAP we are now on does support CIFS and data motion however there will be a small downtime with the CIFS share terminating. Is this correct? Thanks

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