Run all user-guide examples to confirm they work

[trevorhardy]

In preparation for getting the User Guide example incorporated into the CI/CD we already have in place, we need to run through all the supported User Guide examples to make sure they work with the latest packages (including HELICS).

[nathantgray]

Filter clone example does not run because the file ControllerConfig.json does not exist. ControllerConfig.json is called on line 59:
fed = h.helicsCreateMessageFederateFromConfig("ControllerConfig.json")

[nathantgray]

Filter federate has a halting problem. All federates will get stuck after requesting a time grant. The problem is not fixed when preventing the filter from dropping, delaying, interfering, or hacking.

[trevorhardy]

Filter clone example does not run because the file ControllerConfig.json does not exist. ControllerConfig.json is called on line 59: fed = h.helicsCreateMessageFederateFromConfig("ControllerConfig.json")

Added missing files that were just sitting on my computer and apparently had never been commited.

[trevorhardy]

helics_connector using a direct matchfile (JSON or text) is not working for me.

[trevorhardy]

Graphing in dynamic federation example is having some indexing problems.

[trevorhardy]

Graphing in dynamic federation example is having some indexing problems.

Corrected and now working.

[trevorhardy]

The following advanced examples are not currently working with their associated Github issue:

1. Advanced multi-broker - HELICS issue #2721
2. Advanced input and output - HELICS issue #2542
3. Translators - HELICS issue #2562
4. Connector matchfile direct - HELICS issue #2722

[trevorhardy]

OK, I think I've got the examples that need help all tracked with their own HELICS-Examples issues:

1. Fundamental native filter - Fix fundamental native filter example #122
2. Fundamental filter federate - Fix fundamental filter federate example #123
3. Advanced HELICS connector JSON matchfile - helics_connector example using JSON-formatted matchfile doesn't work #124
4. Advanced multi-broker - HELICS multi-broker example not working #125
5. Advanced input-output - Input-output example not working #126

Given this, I'm going to close out this general issue and push our work to the example-specific ones.

[nightlark]

I think sub-issues are enabled if we want to create an issue to track the status of the related tasks.