Deep merge user config with defaults

[gmertes]

When merging default config with the user config, use a deep key-by-key merge instead of just updating the top level keys. If a key exists in both configs, the user config will take priority.

Example:

anemoi-inference run config.yaml --defaults defaults.yaml

# config.yaml
input: mars
output:
  grib:
    path: file.grib
    check_encoding: true

# defaults.yaml
checkpoint: checkpoint.ckpt
output:
  grib:
    encoding:
      some_key: 123
    check_encoding: false

Result:

checkpoint: checkpoint.ckpt
input: mars
output:
  grib:
    path: file.grib
    check_encoding: true
    encoding:
      some_key: 123

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.03%. Comparing base (ff2bd59) to head (762c345).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #107   +/-   ##
========================================
  Coverage    98.03%   98.03%           
========================================
  Files            3        3           
  Lines           51       51           
========================================
  Hits            50       50           
  Misses           1        1           

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