[Fix] Harden validation, configuration, and adapter boundaries

[morluto]

Summary

This PR fixes the validation, configuration-inspection, lifecycle, and adapter-boundary defects tracked in #124–#132.

• Treats expected MCP process termination during protocol shutdown as non-fatal after a successful protocol run, while preserving real run and shutdown errors.
• Makes nil environment handling consistent across execution runners; an empty validation allowlist now inherits the process environment.
• Rejects malformed Claude MCP registrations, non-string Claude arguments, and malformed code-index exclusion globs.
• Guards optional nested GitHub models explicitly during conversion.
• Ensures CLI error returns run deferred Service.Close cleanup.
• Removes confirmed-unused MCP handlers and helpers.
• Stabilizes the process-tree telemetry regression test by giving the child process a deterministic observation window.

Review order

1. 2ed471d — behavioral fixes and regression coverage.
2. 86a149f — confirmed dead-code removal.

Validation

• go test ./...
• go test -race ./internal/evidence -run 'TestMCPStdioRunnerRecordsSDKMilestones|TestExpectedMCPShutdownSignalIsNonFatal|TestExecRunnerCapturesProcessTreeTelemetryAndCleanup' -count=1
• make verify

Fixes #124
Fixes #125
Fixes #126
Fixes #127
Fixes #128
Fixes #129
Fixes #130
Fixes #131
Fixes #132

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