Merge FreeRTOS base code with FPGA I/O timing management code

[npetersen2]

We need to merge #358 and #359 from @codecubepi and @annikaolson into v2-staging branch. Once merged, we will test the merged code to make sure everyone is happy. Then, we will merge into v2 branch.

These should have stable code. Once we get these merged, we can branch back off of v2 to continue work on features like ISRs.

[npetersen2]

We will merge Annika’s FPGA I/O work first (#358) since it will result in a cleaner merge

Then, we will merge Patrick’s Free-RTOS code.

Since Patrick’s code is in a new SDK app, it is completely isolated from Annika’s code…..so the merge will go “smooth,” but nothing will actually be merged.

Finally, the next big task after this "merge" is to actually merge the v1 codebase into the new v2 codebase:

• Move the shared code (sys/ and drv/) into the shared/ folder
• Remove the scheduler.c module from v1 and replace all system level tasks that depend on it with FreeRTOS tasks
• Upgrade the command line interface (CLI) to work in v2 so we can interact with the system dynamically