ACAS-916: Update all html/jade and coffee script usage to bootstrap 3 css

[brianbolt]

Description

• In 2025-3 we updated bootstrap javascript to bootstrap 3 but mistakenly left the bootstrap 2 css in the code base. This led us to believe we updated bootstrap successfully to bootstrap 3 when in fact most of the classes were still using bootstrap2.
• Additionally jQuery file upload was pretty broken because updated it but missed updating the file upload template we were using. This broke the progress bar which I reimplemented and shows a nice progress as part of the upload now.
• These changes are to migrate bootstrap 2 classes to bootstrap 3 and is a significant change.
• The main issues I faced:
  • Forms had completed messed up/no bootstrap styling.
  • Modal dialogue interface changed in bootstrap 3 so dismissing modals and showing them were in a bad place.
  • Some of the custom styling elements like tooltips were broken and need re-implementation.
• I used a ton of AI coding to to fix this but tried to do it in a structured way. Some examples:
  • Experiment Editor, Protocol Editor and Project editor all use a very similar layout so I spent a lot of time on just experiment editor, made sure it was in a good place and then asked copilot to apply the change to all the editors. I did a very similar thing for all the browsers. Noting that as part of the editor changes, I decided that it was easy to create a responsive 2 column, more compact layout and so I checked in those changes here.
  • CurveCurator which was a big mix of css and bootstrap 2 features to get it nice and compact took a decent amount of work to get back in shape but its now pretty responsive and can be shrunk down.
  • CmpdReg bulkloader also had some significant layout changes and like Experiment/Protocol/Project Editors I took the opportunity to create a 2 column layout which is responsive to going down to a small or wide screen.
  • The Single Reg UI seems to be unaffected by any of this so I didn't change anything about it except a seperate PR around the iframed Lot Inventory module.
  • Module menus collapsing feature which isn't widely used was broken so I fixed that.

Related Issue

ACAS-913
ACAS-914
ACAS-916

How Has This Been Tested?

• I did basic testing of the modules as I opened and saved a number of items.
• I verified Dose Response + Curve Curator worked
• Tried to focus on modal showing and hiding since that seemed to be a significant functionality issue in some cases.
• I ran a CmpdReg restandardization, Code tables...etc.
• I verified required fields styling seemed to be working including tool tips.
• I verified uploading a large 8GB file shows a nice progress bar.
• I verified that when made collapsible, the module menus behaved well.
• A lot of the tests I did involved dragging the screen to be smaller to make sure it was responsive.