update windows script to use config file and us-east-1, create separate ec2 script with more options, both launch browser once instance is launched
fix issue when creating security group with ssh access, wait for stochss app to be up before launching browser
add in alarm for new instances
small fix to windows launch script
ask before launching into browser for ec2 script
add stochkit to the path at the end of run.mac/run.ubuntu.sh scripts
complete rewrite of ec2 run script
it now takes a single command and returns after completing that command (currently start, stop, terminate, list)
rewrite windows launch script to make use of the new ec2 script
update AMI IDs for new server images
properly set region for aws cloudwatch
Fixed runscripts for Fedora/linux/ubuntu not writing conf/config correctlike

Modified output messages for run_ec2.py
Merge branch 'windows-ec2-updates' of https://github.com/StochSS/stochss into windows-ec2-updates
Modified run_ec2.py

Suggest we rename to run_windows.py and ditch the current run_windows.py

This version uses the config file approach, but assumes the user is only ever running/stopping/terminating one stochss instance

'list' functionality removed

Verbose output by default
Update button -- Removed!

Simulation manager --
1. Jobs require name now
2. On job submission, user redirected to status page
3. Fixed bug where job datastore object created even if job failed to be created

I also renamed the runscripts so maybe they make more sense to the terminal user? I dunno, these need to be compressed. Anyway, ./run.generic.sh and ./run.generic.html.sh are the new additions. One is meant for the shell, one spits out html output. These really all need compressed down to one file
Merge branch 'windows-ec2-updates' into develop

Conflicts:
	run.mac.sh
Renamed scripts
Bugs still in existance:
1. Revoking user permissions doesn't work (does their data get deleted
when the permissions are removed? Doesn't matter either way, just
curious)
2. No documentation/help on what exactly the model converter does
6. No way to delete reactions
7. Modifying propensity functions doesn't work
8. Convert to population thing needs a way to fail with more errors...
Still buggy and no way for the user to know what went wrong
9. Species initial values are currently not required to be numbers
10. Updating initial vlaues and param v's doesn't always give
indication to the user that the transaction is completed (it should)
11. Propensity column goes off page on reaction editor
12. Reaction editor page looks weird when no species/params defined
13. When the user doesn't save trajectory data, the status page still
tries to plot trajectories
14. More than two inputs to a mass reaction reaction gives a strange
error message
16. Need a way to rename models still

Bugs defeated:
The 'convert to population' and 'duplicate' model buttons by default now save the model
15. Show values/show parameters text on reaction editor page should
not be blue. Looks like links
3. Two hr tags under save changes button
4. Solvers tab in simulation manager needs removed
5. Local plugins needs removed

New Bugs:
Alphabetical sort seems a little backwards... A11, comes before A2
Huh, looks like I totally deleted the run.windows.py scripts
Quick fix to templating mistake
Bugs still in existance
1. Revoking user permissions doesn't work (does their data get deleted
when the permissions are removed? Doesn't matter either way, just
curious)
2. No documentation/help on what exactly the model converter does
8. Convert to population thing needs a way to fail with more errors...
Still buggy and no way for the user to know what went wrong
12. Reaction editor page looks weird when no species/params defined
16. Need a way to rename models still
17. Alphabetical sort seems a little backwards... A11, comes before A2

Bugs defeated in some sneaky way or another....
--
- What I did was make the reactions un-editable. You have to delete and retype them totally. Turns out the delete button was just scrolled off the page :/.
6. No way to delete reactions
11. Propensity column goes off page on reaction editor
7. Modifying propensity functions doesn't work
9. Species initial values are currently not required to be numbers
10. Updating initial vlaues and param v's doesn't always give
indication to the user that the transaction is completed (it should)
14. More than two inputs to a mass reaction reaction gives a strange
error message

-- I removed this option along with the histogram option (histogram can be computed from trajectories)
13. When the user doesn't save trajectory data, the status page still
tries to plot trajectories