Fixes for new Timing Manager mode

[codecubepi]

Addresses #399

This PR includes some important timing/Timing Manager fixes:

• Solves the "current jitter" and control task scheduling problem we observed by switching many scheduler time variables from uint32_t to double and adding some tolerance to the elapsed time check to account for some variation in the double values.
• Fixed a bug created by an incomplete implementation of #400: when no sensors were enabled in the timing manager, new PWM duty ratios were being calculated, but not flushed out in the FPGA. This was because the timing manager's trigger which now flushes the duty ratios required the all_done signal to be high, but that required at least one sensor to be enabled. The fix was to remove this unnecessary qualification.
• Adds an expected_tick_delta() function in the timing manager, which calculates the expected time between scheduler interrupts, based on the user's PWM switching frequency, alignment settings, and enabled sensors. This is used in place of the real-time get_tick_delta() function where we do not need real-time data.
• Adds a debug counter to the timing manager which counts the number of triggers sent. This value can be LOGged or retrieved via the command interface.
• Moved the timing manager initialization up in main(), as to not overwrite anything the user would initialize in their app_init() function.
• Fixes a bad debug to GPIO port connection in the REV E block design

This comment on the v1.3 WIP Pull Request has the remaining items before we release.

[codecubepi]

We recently merged #400 in v1.3-staging, so fix-tm-mode got rebased and force-pushed.

[codecubepi]

@npetersen2

I think this is ready for a proper review and hopefully a merge into v1.3-staging, so I'll remove the Draft status. Since a fix has not been found yet for the sensor enable/disable bug, that has been split off into a new issue: #402

Please read the top comment on this PR conversation for a full list of changes in this PR.

[npetersen2]

Let's get this merged to v1.3-staging so @anirudhupadhyaya code can point to the latest v1.3-staging branch