Basic server, hoooks up to Q.

Pushing so Zach and Robert can work off same branch.
fixed naming
rename index.html index.jsp
Update and rename codonPDX.java to CodonPDX.java
Mucking with the path names.  There is a bug where url/app/ doesn't load the js files properly.

We might need to have all static content be served at an absolute path.
Starting the post response.
Starting the post response. Times two.
Got a basic file writing in the form.html in codonpdx-zac.
gradle with new item

form handles file uploads

started some of the receiving end of those uploads
Results/UUID queries DB for results with that UUID, spits back JSON
Got a basic file upload, still need to stick in proper area of server.
Results/UUID queries DB for results with that UUID, spits back JSON
Read in user input, parse it, schedule a task and return the UUID.
merged master to this.

The one-to-one results is finished.

Urls of the type: url:8080/codonpdx/UUID/assession  return the JSON needed to display a one to one comparison.
for 1-1 JSON, the counts are now the ratio, grouped by amino acid.  Will wrk for mutliple codon tables.
Removed cruft FileUploadHandler
towards a saner build.gradle
Merge branch 'web_app_work' of github.com:PDX-Flamingo/codonpdx into web_app_work
build.gradle now generates a proper war file
Merge pull request #6 from PDX-Flamingo/web_app_work

Web app work