Harmonize description of time series, infection states etc in documentation

[mknaranja]

Provide a description of requested documentation changes.

In the documentation, time series, infection states, compartmental models (and flow models) are sometimes described in "normal" language, sometimes TimeSeries, CompartmentalModel, ... (in reference to code objects)

While this in-consistency is too some extent meaningful, all occasions of the above should be checked for either referring to the precise code object or not.

In addition, all code object references should be put in code style and not in bold face.

[mknaranja]

Before creating a branch, #1531 should be merged as there are already some improvements included.