Update cron script paths

[DragosIorgulescu]

• [x] update script paths to reflect the current dir structure
• [x] check log files are being generated if they don't exist

[ahamelers]

Related issue in #3135 Documentation will need updating, too. Let me know if you want to divide up this work or if you've got it under control.

app/views/stash_engine/submission_queue/index.html.erb:  <em>~/apps/ui/releases/hold-submissions.txt</em> in our current directory structure.</p>
app/services/stash_engine/status_dashboard/submission_status_service.rb:      LOG_FILE = '/apps/dryad/apps/ui/current/log/merritt_status_updater.log'
app/services/stash_engine/status_dashboard/db_backup_service.rb:      BACKUP_DIR = '/dryad/apps/ui/shared/cron/backups'
config/script/delayed_job.sh:    export HOME=/apps/dryad
config/script/delayed_job.sh:    export RAILS_ROOT=/dryad/apps/ui/current
config/script/long_jobs.sh:    export HOME=/apps/dryad
config/script/long_jobs.sh:    export RAILS_ROOT=/dryad/apps/ui/current
config/deploy.rb.pre_puppet:set :deploy_to, '/apps/dryad/apps/ui'
config/deploy.rb.pre_puppet:set :default_env, { path: '/apps/dryad/local/bin:$PATH' }
config/deploy.rb.pre_puppet:      res1 = capture "ls /apps/dryad/apps/ui/shared/config/*.key -1"
config/deploy.rb.pre_puppet:      execute "mkdir -p /apps/dryad/apps/ui/shared/cron"
config/deploy.rb.pre_puppet:      execute "cp /apps/dryad/apps/ui/current/cron/* /apps/dryad/apps/ui/shared/cron"
config/deploy.rb:set :deploy_to,        ENV['DEPLOY_TO']       || '/dryad/apps/ui'
cron/counter.sh:# may have some environment problems, maybe needs to be run as interactive shell or see /apps/dryad/apps/ui/unbloat.sh for setting environment
cron/counter.sh:cd /apps/dryad/apps/ui/current
cron/README.md:The files deploy with the code (in `apps/ui/current`), but the logs and shared items are in
cron/README.md:*/5 * * * * /apps/dryad/apps/ui/current/cron/every_5.sh stage >> /home/ec2-user/deploy/shared/cron/logs/cron.log 2>&1
cron/README.md:00 12 * * * /apps/dryad/apps/ui/current/cron/daily.sh stage >> /home/ec2-user/deploy/shared/cron/logs/cron.log 2>&1
cron/README.md:00 21 * * 0 /apps/dryad/apps/ui/current/cron/weekly.sh stage >> /home/ec2-user/deploy/shared/cron/logs/cron.log 2>&1
cron/README.md:scp <user>@<domain>:/apps/dryad-prd-shared/json-reports/* .
documentation/ruby_version_server_upgrade.md:cd ~/apps/ui/releases/
documentation/ruby_version_server_upgrade.md:cd ~/apps/ui/
documentation/ruby_version_server_upgrade.md:ln -s /apps/dryad/apps/ui/releases/temp-cap current
documentation/server_maintenance/storage.md:touch /apps/dryad/apps/ui/releases/hold-submissions.txt
documentation/server_maintenance/storage.md:rm /apps/dryad/apps/ui/releases/hold-submissions.txt
documentation/server_maintenance/troubleshooting.md:`less /apps/dryad/apps/ui/current/log/production.log`
documentation/server_maintenance/deploying_new_code.md:files into `~/apps/ui/current`.
documentation/server_maintenance/deploying_new_code.md:- On 2c, run `~/bin/long_jobs.dryad drain`.  It touches the defer_jobs.txt and hold-submissions.txt files in `~/apps/ui/releases`.
documentation/server_maintenance/deploying_new_code.md:- On 2a, touch `~/apps/ui/releases/hold-submissions.txt`
documentation/server_maintenance/deploying_new_code.md:- Remove `~/apps/ui/releases/hold-submissions.txt` on 2a.
documentation/reports.md:cd /apps/dryad/apps/ui/current
documentation/reports.md:cp /apps/dryad/apps/ui/current/shopping* ~/journal-payments/shoppingcart/
documentation/tenants.md:       `/apps/dryad/local/shibboleth-sp/var/InCommon-metadata.xml`. If the
documentation/tenants.md:    directory `/apps/dryad/local/shibboleth-sp/etc/shibboleth`.
documentation/counter_overview.md:  - It produces a JSON report (see `apps/ui/shared/cron/counter-json`).
documentation/counter_stats.md:  - We save reports to `/apps/dryad-prd-shared/json-reports`
documentation/zenodo_integration/delayed_jobs.md:  the file `defer_jobs.txt` in `~/apps/ui/releases` and it will not submit new things to zenodo while it's there.
lib/tasks/embargo_fix.rake:    File.readlines('/apps/dryad/embargoIssues.txt').each do |line|
lib/tasks/embargo_fix.rake:    File.readlines('/apps/dryad/embargoIssues.txt').each do |line|
lib/tasks/counter/log_combiner.rb:        # ssh dryad@uc3-dryaduix2-prd-2c.cdlib.org "rm -f /apps/dryad/apps/ui/current/log/counter_2020-09-01.log"
lib/tasks/counter/log_combiner.rb:          log_filenames = `ssh #{USERNAME}@#{host} "cd /apps/dryad/apps/ui/current/log/; ls counter_*.log -1a"`.split("\n")
lib/tasks/counter/log_combiner.rb:              `ssh #{USERNAME}@#{host} "rm -f /apps/dryad/apps/ui/current/log/#{fn}"`

[DragosIorgulescu]

No problem, I'll knock this out tomorrow