Incremental updates from MWGR#4 - v2

Description

This MR includes the various developments and bugfixes required to run reliability in miniDAQ and Global at p5 during MWGR4.

Improvements:

(Features)

1. Merge the gem::hardware::optohybrid::OptoHybridManager and gem::hardware::amc::AMCManager into gem::hardware::AMCManager
2. Separate AMC recovery and clocks reset
3. Support a single board per AMC manager (allow trivial parallelization)
4. Use the OptoHybrid mask when establishing the communication
5. Add an option to automatically disable the bad chambers

(Robustness)

1. Attempt to check the GBT lock 20 times before programming
2. Check the SCA status after module reset
3. Wait for TTC hard reset completion during configuration
4. Check the GEM loader counters after OH FPGA programming

(Speed)

1. Use TTC calibration mode from AMC for latency scan
2. Use RPC method confCalPulse to disable calibration pulses of VFAT channels

(Configuration)

1. Add layer 2 in the gem904daq04 xDAQ configuration
2. Define better the xDAQ application numbers and port

Bug fixes:

1. Set the BX offset between the AMC13 and AMC
2. Allow transitioning from one stable state to itself
3. Update latency value only once (introduced while merging the OptoHybrid manager and AMC manager)
4. Disable external PLL reset (temporary workaround for firmware bug)

Closes #90 (closed).

How Has This Been Tested?

Tested on the integration setup in b904 and during miniDAQ and global runs at p5.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.