Replace RuntimeError exceptions

The current code over-uses the python exception hierarchy, especially `RuntimeError` exceptions, where custom exception classes would be better. This makes it difficult to differentiate between legitimate errors and known or expected conditions.

For example, `source/fab/tools/tool.py` contains the following:

```py
if self._is_available is False:
raise RuntimeError(f"Tool '{self.name}' is not available to run "
f"'{command}'.")
try:
res = subprocess.run(command, capture_output=capture_output,
env=env, cwd=cwd, check=False)
except FileNotFoundError as err:
raise RuntimeError(f"Command '{command}' could not be "
f"executed.") from err
if res.returncode != 0:
msg = (f'Command failed with return code {res.returncode}:\n'
f'{command}')
if res.stdout:
msg += f'\n{res.stdout.decode()}'
if res.stderr:
msg += f'\n{res.stderr.decode()}'
raise RuntimeError(msg)
```

Which prevents the caller from determining whether the condition was a configuration issue, whether it was a legitimate failure because the compiler being targeted was not installed, or whether an error occurred running the command.