refactor: consolidate command runtime and injected dependencies

[qwrobins]

Summary

• Consolidate common command/runtime options, context construction, and retry normalization.
• Forward injected stdout/stderr across handlers and diagnostics, and use the injected transport for OAuth refresh as well as GraphQL.
• Split issue commands by responsibility while retaining registry dispatch and existing public exports/contracts.
• Add runtime documentation and regression coverage for injected streams, transport, profile precedence, and concurrent invocations.

Closes #183

Validation

• bun run typecheck
• bun run build
• bun run test — 933 passed, 1 skipped
• git diff --check

Greptile Summary

This PR consolidates command execution around a shared runtime context while preserving command contracts.

• Centralizes profile resolution, retry normalization, GraphQL execution, injected transport, and output streams.
• Splits issue handling into responsibility-focused modules while retaining registry dispatch and public exports.
• Routes diagnostics, pagination, file-transfer output, and schema freshness warnings through injected streams.
• Defines last-occurrence precedence for the --max and --limit aliases and documents the download commit boundary.
• Adds regression coverage for injected dependencies, concurrent invocation isolation, pagination aliases, and file-transfer cancellation behavior.

Confidence Score: 5/5

The PR appears safe to merge, with no outstanding actionable defects identified in the changes since the previous review.

The pagination follow-up keeps each winning value paired with its alias metadata across option segments, and the file-transfer follow-up accurately documents the existing atomic commit behavior. No repository-rule violations or accepted new security findings remain.

Important Files Changed

Filename	Overview
src/cli/main.ts	Forwards injected runtime dependencies and normalizes pagination aliases according to argument order.
src/core/runtime/command-context.ts	Provides the shared command lifecycle for profile resolution, transport, retries, and output.
src/commands/issue.ts	Retains issue registry dispatch and public contracts while delegating implementation to focused modules.
src/core/io/file-transfer.ts	Documents the non-cancellable atomic rename boundary without changing its established success semantics.
tests/cli/runtime.test.ts	Covers injected runtime behavior and pagination-alias precedence across option positions.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  CLI[CLI argument parsing] --> Registry[Command registry]
  Registry --> Options[Shared command options]
  Options --> Context[CommandContext]
  Context --> Profile[Profile resolution]
  Context --> Retry[Retry normalization]
  Context --> Transport[Injected transport]
  Context --> IO[Injected stdout and stderr]
  Context --> Handler[Curated or generated handler]
  Handler --> Output[Stable command output]

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_{Reviews (3): Last reviewed commit: "address greptile review feedback (greplo..." | Re-trigger Greptile}

[qwrobins]

@greptile review

[qwrobins]

Addressed the pagination-alias finding: aliases now normalize in token order before merging leading and command-position options, so the last --max/--limit wins. Regression tests cover both orders, both positions, equals syntax, repetitions, and validation diagnostics. Docs and bundled skills are updated.

For the summary's final-rename observation: the existing cancellation check immediately before rename is intentional. Node/filesystem rename has no cancellation API, and racing it against abort would allow a destination replacement after reporting failure. The atomic commit must report its actual result once dispatched. Added an explicit code/docs contract and a regression test proving cancellation during rename still reports the successful committed replacement. No unsafe rollback or misleading post-commit abort was introduced.

Validation after merging current main and these changes: typecheck/build pass; 933 tests passed, 1 skipped.