If it helps anyone having this issue, I started using railsless for deploy, 
along with ThePixelDeveloper's Capistrano recipe at 
https://gist.github.com/ThePixelDeveloper/211105

On Wednesday, February 20, 2013 4:24:33 PM UTC, dbray wrote:
>
> You will need to override the cap variable shared_children in order to 
> omit 'system' from symlink activities during deploy. 
>
> On Feb 20, 2013, at 6:36 AM, bsod99 <[email protected] <javascript:>> 
> wrote:
>
> Sorry for the delay on this - should there be something in the shared/pids 
> folder? mine are always empty (running ls -a). One thing which may or may 
> not be linked to the issue, is that capistrano is creating a "system" 
> folder, in shared. The framework I use for my sites also has a system 
> folder, which contains all the core framework files which are never edited. 
> So my releases folder would have the following for example:
>
> app_public
> app_admin
> public_html
> system
> modules
>
> And my shared folder would have
>
> app_public -> containing some non-versioned config stuff symlinked to 
> currnet
> app_admin -> same for this
> public_html -> same 
> cached-copy -> capistrano
> log -> capistrano
> pids -> capistrano
> system -> capistrano
>
> On Thursday, 7 February 2013 16:44:41 UTC, dbray wrote:
>>
>> Inspecting the contents and comparing the pids specified in the files vs 
>> the ones that are running may give you clues to the problem. 
>>
>> Make a note of your pids pre-deploy; do the deploy then compare the pids 
>> previous; to the current pids; and to the pids in the directory. 
>>
>> On Feb 7, 2013, at 6:45 AM, bsod99 <[email protected]> wrote:
>>
>> Further update on this, in case it helps pinpoint the issue(s) - when an 
>> error (as described above) arises after a deployment, if I remove the 
>> releases/cached-copy/log/pids folders and run deploy:setup and deploy, my 
>> sites work correctly. 
>>
>> On Wednesday, 6 February 2013 21:49:09 UTC, bsod99 wrote:
>>>
>>> I'm on CentOS 6, standard LAMP setup. It's really puzzling.
>>>
>>> I wonder if I should just start afresh, as I've been messing about with 
>>> the deployment script a fair bit. 
>>>
>>> On Wednesday, 6 February 2013 17:46:37 UTC, dbray wrote:
>>>>
>>>> What web server are you using. I experienced something similar with 
>>>> unicorn. Because of its forking the master process it had already resolved 
>>>> the symlink to a specific directory. Everything would work fine until the 
>>>> original dir the master was originally started from finally got cleaned 
>>>> up. 
>>>>
>>>> I used to use passenger and it had similar issues until they 
>>>> incorporated a patch to re-evaluate the symlink for each fork. 
>>>>
>>>> On Feb 6, 2013, at 4:30 AM, bsod99 <[email protected]> wrote:
>>>>
>>>> Thanks, switched to latest_release. All the targets exist in shared, 
>>>> and 'cap deploy:shared_symlinks' is executing successfully during the 
>>>> deployment. Checking the symlinks after shows they are correct. 
>>>>
>>>> The cap task isn't raising any errors. The issue is that non-shared 
>>>> core classes in my application are sporadically not found after a 
>>>> deployment, even though these files are sitting in the current release in 
>>>> the correct place. Also, upon re-deploying, sometimes the error can be 
>>>> another core class which isn't found. This just adds to the confusion in 
>>>> that the error isn't consistent. 
>>>>
>>>> For testing, I've set keep_releases to 1 for now - on a couple of 
>>>> sites, deployments are working fine, but on another, I'm having the issue 
>>>> described above. The deployment scripts are practically identical.
>>>>
>>>>
>>>>
>>>> On Tuesday, 29 January 2013 17:26:33 UTC, dbray wrote:
>>>>>
>>>>> It should be #{latest_release} not #{release_path}
>>>>>
>>>>> release_path only works during a deploy; latest_release will work all 
>>>>> the time. 
>>>>>
>>>>> See: 
>>>>>
>>>>>
>>>>> https://github.com/capistrano/capistrano/blob/master/lib/capistrano/recipes/deploy.rb
>>>>>
>>>>> Have you ensured that all the targets in shared exist before 
>>>>> attempting to create the symlinks?
>>>>>
>>>>> What isn't working about it?
>>>>>
>>>>> Are you invoking 'cap deploy:shared_symlinks' then see my suggestion 
>>>>> above. 
>>>>>
>>>>> Is the cap task raising an error; post a copy of a failed run. 
>>>>>
>>>>> Is the task executing but you just don't end up with the symlinks?
>>>>>
>>>>> Are there files pre-existing in the release directory from checkout; 
>>>>> you need to remove them in order to recreate them as symlinks. 
>>>>>
>>>>> On Jan 29, 2013, at 3:30 AM, bsod99 <[email protected]> wrote:
>>>>>
>>>>> Alas, this still isn't correct - symlinking definitely a bit messed 
>>>>> up, Can anyone see what is wrong with this staging.rb script? 
>>>>> http://pastie.org/5927281
>>>>> I must still have the order wrong...thanks for any help
>>>>>
>>>>>
>>>>> On Thursday, 24 January 2013 09:47:59 UTC, bsod99 wrote:
>>>>>>
>>>>>> Thanks for all the replies. I followed dbray's advice and kept 
>>>>>> releases at, and adjusted sequencing to:
>>>>>>
>>>>>> after "deploy:update", "deploy:symlink_shared"
>>>>>> after "deploy:restart", "deploy:cleanup"
>>>>>>
>>>>>> This seems to be working fine (and makes sense, having thought 
>>>>>> through more carefully about what each is doing)
>>>>>>
>>>>>> On Thursday, 24 January 2013 02:42:51 UTC, dbray wrote:
>>>>>>>
>>>>>>> Keep releases should be 2 at minimum in my opinion
>>>>>>>
>>>>>>> On Jan 23, 2013, at 9:26 AM, bsod99 <[email protected]> wrote:
>>>>>>>
>>>>>>> I followed the advice in another post about how to clean up old 
>>>>>>> capistrano releases, however, i've realised that the way I've 
>>>>>>> implemented 
>>>>>>> this has messed up the paths in my application (just on a staging site 
>>>>>>> thankfully!). I am using the code below in my config/deploy/staging.rb 
>>>>>>> script, but it can't be running at the correct point, as after 
>>>>>>> deployment I 
>>>>>>> end up with application failing as it's trying to load classes from 
>>>>>>> earlier 
>>>>>>> releases. If I remove the keep_releases line and the one below, and 
>>>>>>> redeploy, everything works again. Has anyone come across this issue?
>>>>>>>
>>>>>>> set :use_sudo, false
>>>>>>> set :keep_releases, 1
>>>>>>> after "deploy:update", "deploy:cleanup"
>>>>>>>
>>>>>>> namespace :deploy do
>>>>>>>   task :symlink_shared do
>>>>>>>     // run some commands i need
>>>>>>>   end
>>>>>>> end
>>>>>>>
>>>>>>> before "deploy:restart", "deploy:symlink_shared"
>>>>>>>
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