Replace to_dict with as_dict (#4352)

* deprecate to_dict

* deprecate JDFTX with 6 months grace period

* update compatibility log

* more hidden replacement

* revert to to_dict for dataframe

* deprecate to_xxx in abitimer

* directly rename dev/helper functions

* more as_xxx

* fix typo

* deprecate composition

* use args and kwargs to pass thru, would loss autocomplete

* more to_xxx

* last batch as_xxx

* as_table_str

* update usage in tests

* fix some leftover

* add naming convention note in contributing md

* update compatibility log

* TO BE REVERTED: mark future warning as error

* add dummy docstring

* fix some

* should be everything to fix

* revert everything first

* Revert "update compatibility log"

This reverts commit 87ab51c.

* deprecate to_dict

* deprecate JDFTX with 6 months grace period

* change other to dict in core

* update compatibility log

* better alias

* migrate internal usage

* regenerate docs

Author: DanielYang59