Rename internal variables and methods to start with _

[ondras12345]

As suggested in #254

I wasn't sure about these, so I left them alone:

• Should isParameterChangeable() be part of the public API?
• Should setTempDirectory() be part of the public API?
• Should setCommandLineOptions() be part of the public API? (I.e. should it be allowed to set extra options after the object is constructed? We already have a commandLineOptions arg in the constructor.)

To minimize future merge conflicts, and for me to be able to take advantage of pre-commit while making these changes, this PR is based on #289.

[ondras12345]

Converted to draft, probably best to wait for #289 and #295 before fixing merge conflicts here.

[ondras12345]

Rebased and fixed all conflicts. If the answer to all 3 questions in the original comment is 'yes', then this PR is ready for review and merge. If not, I'll rename the functions to indicate that they are internal.

[adeas31]

@arun3688 can you please answer the above questions and review this PR.

[syntron]

Based on PR #312 the method isParameterChangeable() is needed as part of the public API!

[syntron]

@ondras12345 just as a side note: if these variables are modified / renamed - would it be possible to change them to lowercase, with words separated by underscores? I have tried to not touch such cases as I'm not sure if there is any rule regarding this within OMPython. However, here we would change it to private and, thus, have all possibilities to change it without touching a public API