fix: address issues from PR #2 merge

[ourines]

Summary

• Add backward-compatible config migration via custom UnmarshalJSON — old flat-field configs are auto-migrated to the new env map format
• Fix JSON injection in TestAPIConfig by replacing fmt.Sprintf with json.Marshal
• Fix format string bugs in RunConfigSet/RunConfigGet where %s was never substituted
• Remove unused cfg parameter from SetEnvironmentVarsWithConfig
• Fix import ordering in cobra.go
• Replace log.Printf with fmt.Fprintf for consistent logging style

Test plan

• Verify old-format config.json loads correctly and env vars are migrated
• Verify codes test works with model names containing special characters
• Verify codes config get invalidkey shows the key name in error message
• Verify go build ./... passes

Fixes #4, Fixes #5, Fixes #6

🤖 Generated with Claude Code

Summary by CodeRabbit

• Chores

  • Refactored environment-variable/config handling for clearer behavior and maintainability.
  • Added automatic migration of legacy configuration fields so older configs continue to work.

• Bug Fixes

  • Standardized error messaging for unknown configuration keys.
  • Improved how external processes are launched so commands run in the intended directory.

[coderabbitai]

📝 Walkthrough

Walkthrough

Adds JSON unmarshaling to migrate legacy flat API config fields into the new env map, fixes JSON-building and format-string bugs, removes an unused parameter from SetEnvironmentVarsWithConfig and updates its call sites, and adjusts import/logging ordering.

Changes

Cohort / File(s)	Summary
Config migration & env handling internal/config/config.go	Added UnmarshalJSON to detect/migrate legacy ANTHROPIC_BASE_URL/ANTHROPIC_AUTH_TOKEN into Env; replaced string-based test request construction with structured types + json.Marshal; removed log usage in favor of fmt.Fprintf(os.Stderr, ...); adjusted imports.
Command callsites & error formatting internal/commands/commands.go	Updated SetEnvironmentVarsWithConfig call sites to the new single-arg signature; changed process invocation to set cmd.Dir = dir; fixed format-string usage by constructing error messages with fmt.Sprintf before passing to ui.ShowError.
Import ordering internal/commands/cobra.go	Reordered standard-library imports (moved strings into stdlib group) to satisfy usage in SkipPermissionsSetCmd (no functional change).

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Possibly related PRs

• feat: enhance environment variable support and related functionalities #2: Introduced the original config refactor (env map) and the SetEnvironmentVarsWithConfig changes that this PR migrates/fixes.

Poem

🐇 I nibbled through old JSON lines,
Pulled tokens from forgotten mines,
Cleaned the strings and tuned the flow,
Pruned a param — now onward we go,
The warren hums with brighter signs.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 71.43% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'fix: address issues from PR #2 merge' clearly summarizes the main focus of the pull request, which consolidates fixes for three specific issues identified after PR #2.
Linked Issues check	✅ Passed	All coding requirements from linked issues #4, #5, and #6 are met: custom UnmarshalJSON for config migration, JSON injection fix via json.Marshal, format string fixes, unused parameter removal, import ordering correction, and logging style alignment.
Out of Scope Changes check	✅ Passed	All changes directly address the three linked issues without introducing unrelated modifications. Changes are confined to fixing the identified problems in cobra.go, commands.go, and config.go.

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✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/pr2-issues

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[ourines]

@copilot

[Copilot]

@ourines I've opened a new pull request, #8, to work on those changes. Once the pull request is ready, I'll request review from you.