Imported configuration values set via apply_default() are not recognized as modified, causing fallback to defaults during import #1110

Description:

When importing a Malcolm configuration file using install.py (e.g., with --import-malcolm-config-file), the configuration items present in the file are read and values are set via the apply_default() method in MalcolmConfig. However, these values are not marked as modified internally.

As a result, the import process treats these keys as missing and falls back to default values, logging warnings such as:

Configuration item not found in settings file, using default:
This behavior occurs even when importing a freshly exported default configuration file without any changes.

Steps to Reproduce:

Export the default configuration file using:

python3 ./scripts/install.py --export-malcolm-config-file default.json
Import the same file back with debug enabled:

python3 ./scripts/install.py --configure --non-interactive --import-malcolm-config-file default.json --debug
Observe warnings about configuration items not found and usage of defaults, despite the keys being present.

Expected Behavior:

Imported configuration values should be recognized as user-supplied (i.e., marked as modified) and not treated as missing or defaulted.

Root Cause (suggested):

The import code calls MalcolmConfig.apply_default(key, value) to set imported values, which does not mark the configuration items as modified. Instead, it should use a method like MalcolmConfig.set_value(key, value) that flags the keys as modified.

Suggested Fix:

Change the import logic to use set_value() (or equivalent) instead of apply_default() when applying user-imported configuration values.

Additional Information: