cli: delete dead root-package code and its dedicated tests

All unreachable from the CLI entry points (x/tools deadcode + reference grep), exercised only by tests written for them:

• metadata.go removed whole: cli-package task-checkpoint IO was a dead duplicate of the strategy package's equivalents.
• explain.go: runExplainDefault/runExplainBranchDefault wrappers (superseded by runExplainBranchWithFilter), formatSessionInfo, hasCodeChanges (superseded by hasAnyChanges).
• git_operations.go: GetMergeBase, findNewUntrackedFiles.
• hooks.go: the pre/post task-hook parse+log family and its orphaned input types — prod parses subagent hooks via parseSubagentCheckpointHookInput.
• status_style.go: single-row metadataRow (prod renders via metadataRows/metadataRowsWithWidth).
• trail_cmd.go/trail_context_cache.go/trail_resume_cmd.go: test-only wrappers over the live validated/scoped/WithSkipped variants; tests covering real behavior were repointed at the live functions instead of deleted (trail list options, enablement-cache TTL/scope matching, resume-context sorting and command building).
• transcript.go: package-level GetTranscriptPosition + TranscriptPosition (the same-named agent-interface methods are the live path).

Left in place pending a maintainer decision: resumeSingleSession and ExtractTodoContentFromToolInput — both look like missing wiring rather than leftovers (no call site ever existed in this repo's history).