[codex] fix config precedence resolution

[abtreece]

Summary

• Track whether config options came from CLI arguments or environment variables before merging TOML
• Apply TOML only when the option was not explicitly supplied by CLI/env
• Move backend node defaults after TOML resolution so config-file nodes can apply
• Add precedence regression coverage for explicit default-valued CLI/env settings

Why

Fixes #601. The old merge logic compared parsed values against hard-coded defaults, so an explicit default-valued CLI/env setting could be treated as unset and overwritten by TOML.

Validation

• go test ./cmd/confd
• go test ./...

[codecov]

Codecov Report

❌ Patch coverage is 66.66667% with 40 lines in your changes missing coverage. Please review.
✅ Project coverage is 71.01%. Comparing base (78e3430) to head (ce45a61).

Files with missing lines	Patch %	Lines
cmd/confd/config.go	62.74%	10 Missing and 28 partials ⚠️
cmd/confd/cli.go	88.88%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #609      +/-   ##
==========================================
+ Coverage   70.83%   71.01%   +0.17%     
==========================================
  Files          53       53              
  Lines        5644     5682      +38     
==========================================
+ Hits         3998     4035      +37     
- Misses       1418     1419       +1     
  Partials      228      228              

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[Copilot]

Pull request overview

This PR fixes configuration precedence between CLI flags, environment variables, and the TOML config file by tracking whether options were explicitly provided via CLI/env (even when set to their default values), and only applying TOML values when an option wasn’t explicitly supplied. It also delays backend node defaulting until after TOML resolution so config-file-provided nodes can take effect.

Changes:

• Track explicit config sources (CLI vs env) using Kong parse context metadata and gate TOML application accordingly.
• Apply backend node defaults after TOML merge to ensure config-file nodes aren’t overridden by command defaults.
• Add regression tests covering explicit default-valued CLI/env options and backend precedence behavior.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.

File	Description
cmd/confd/config.go	Introduces explicit-source tracking + shouldApplyTOML() to correctly resolve precedence using TOML metadata and Kong parsing info.
cmd/confd/cli.go	Captures explicit-source info via AfterApply() and centralizes backend node defaults in applyBackendDefaults() after TOML merge.
cmd/confd/config_test.go	Adds precedence regression tests for explicit default-valued CLI/env settings and backend default-vs-TOML precedence.
cmd/confd/cli_test.go	Updates precedence test setup for new explicit-source tracking and adds direct coverage for applyBackendDefaults().

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