Honor --debug flag in vmcp

[jhrozek]

Summary

• Why: vmcp's --debug CLI flag was effectively a no-op. cmd/vmcp/main.go called viper.GetBool("debug") before app.NewRootCmd().ExecuteContext(ctx) ran, so the flag binding — which happens inside NewRootCmd — had not yet been applied. The logger was always initialized at INFO level, and slog.Debug calls in dependent packages were invisible regardless of whether the flag was passed.
• What: Move logger initialization into the root command's PersistentPreRunE, which runs after cobra has parsed flags and populated viper. Keep a minimal INFO-level default logger in main() so errors emitted before cobra's Execute still produce structured output.

This matches the pattern already used in cmd/thv/app/commands.go for the main thv CLI — the same bug was fixed there previously.

Type of change

• Bug fix

Test plan

• Linting (task lint-fix)
• Manual verification: built binary, ran vmcp --debug version (DEBUG line present) vs vmcp version (no DEBUG), confirmed the difference.

Changes

File	Change
cmd/vmcp/main.go	Remove the ineffective pre-flag-parse viper.GetBool("debug") block; install a minimal INFO-level default logger instead.
cmd/vmcp/app/commands.go	Add PersistentPreRunE on the root command that reads the parsed --debug flag and reinstalls the logger at the correct level.

Does this introduce a user-facing change?

Yes, in the sense that vmcp --debug now actually enables debug logging. Previously it was silently ignored.

Special notes for reviewers

• Mirrors the existing fix in cmd/thv/app/commands.go.
• logging.New is idempotent — calling it twice (once in main, once in PersistentPreRunE) is safe.
• Verified during the end-to-end test of Fix Cedar upstream-claim evaluation on VirtualMCPServer #5002 (the Cedar Resolved JWT claim keys log only became visible once this fix was in place).

Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 0% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 69.05%. Comparing base (cffe934) to head (dff85fb).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
cmd/vmcp/app/commands.go	0.00%	10 Missing ⚠️
cmd/vmcp/main.go	0.00%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #5008      +/-   ##
==========================================
+ Coverage   69.02%   69.05%   +0.02%     
==========================================
  Files         554      554              
  Lines       73075    73083       +8     
==========================================
+ Hits        50443    50470      +27     
+ Misses      19620    19603      -17     
+ Partials     3012     3010       -2     

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