fix: Prevent config option from reverting modified configurations

[sunjq1]

Summary

This PR fixes an issue where uncommented default configuration options (such as nvidia-container-runtime.debug) were being automatically re-commented when running nvidia-ctk config(without the --set flag), even if the user had explicitly enabled them in the configuration file.

Problem

The current implementation of commentDefaults() relies on a valuesSet map to track which configuration keys have been explicitly modified. However, when loading an existing configuration file from disk, the valuesSet map remained empty.

As a result, if a user manually uncommented a default setting without changing its value(e.g., nvidia-container-runtime.debug = "/var/log/nvidia-container-runtime.log"), or uncommented with the --set flag, the toolkit would:

• Fail to recognize the key as "user-set" during the loading phase.
• Match the value against the internal hardcoded defaults.
• Re-apply the # comment prefix during the Save() operation, effectively reverting the user's manual configuration.

Changes

• Modified the configuration loading logic to differentiate between loading an existing file and generating a fresh default configuration.
• Updated loadConfigToml() to traverse the TOML tree after successfully reading from a file, populating the valuesSet map with all keys present in the file.

Testing Performed

• Verified that running nvidia-ctk config --in-place no longer re-comments uncommented lines in /etc/nvidia-container-runtime/config.toml.
• Verified that nvidia-ctk config default still generates a standard template with the correct comments and default values.

Before Fix

$ ./nvidia-ctk config default -o /etc/nvidia-container-runtime/config.toml 
$ ./nvidia-ctk config |grep debug
#debug = "/var/log/nvidia-container-toolkit.log"
#debug = "/var/log/nvidia-container-runtime.log"
$ ./nvidia-ctk config --set nvidia-container-runtime.debug=/var/log/nvidia-container-runtime.log --in-place
$ ./nvidia-ctk config |grep debug
#debug = "/var/log/nvidia-container-toolkit.log"
#debug = "/var/log/nvidia-container-runtime.log"

After Fix

$ ./nvidia-ctk config default -o /etc/nvidia-container-runtime/config.toml 
$ ./nvidia-ctk config |grep debug
#debug = "/var/log/nvidia-container-toolkit.log"
#debug = "/var/log/nvidia-container-runtime.log"
$ ./nvidia-ctk config --set nvidia-container-runtime.debug=/var/log/nvidia-container-runtime.log --in-place
$ ./nvidia-ctk config |grep debug
#debug = "/var/log/nvidia-container-toolkit.log"
debug = "/var/log/nvidia-container-runtime.log"

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[elezar]

As a general comment, could we add unit tests to validate the original behaviour and then verify that the fix addresses this.

[sunjq1]

As a general comment, could we add unit tests to validate the original behaviour and then verify that the fix addresses this.

I have updated the PR with a unit test: TestLoadConfigToml in api/config/v1/toml_test.go.

Before Fix

$ go test
--- FAIL: TestLoadConfigToml (0.00s)
    --- FAIL: TestLoadConfigToml/save_uncommented_configuration_items_to_file (0.00s)
        toml_test.go:388: 
                Error Trace:    nvidia-container-toolkit/api/config/v1/toml_test.go:388
                Error:          Not equal: 
                                ...
                                Diff:
                                --- Expected
                                +++ Actual
                                @@ -7,3 +7,3 @@
                                 [nvidia-container-cli]
                                -debug = "/var/log/nvidia-container-toolkit.log"
                                +#debug = "/var/log/nvidia-container-toolkit.log"
                                 environment = []
                                @@ -18,3 +18,3 @@
                                 [nvidia-container-runtime]
                                -debug = "/var/log/nvidia-container-runtime.log"
                                +#debug = "/var/log/nvidia-container-runtime.log"
                                 log-level = "info"
                Test:           TestLoadConfigToml/save_uncommented_configuration_items_to_file
FAIL
exit status 1
FAIL    github.com/NVIDIA/nvidia-container-toolkit/api/config/v1        0.010s

After Fix

$ go test
PASS
ok      github.com/NVIDIA/nvidia-container-toolkit/api/config/v1        0.009s