MVP alpha.14: Enhanced adapter commands/skills and other enhancements.

[ZebulonRouseFrantzich]

This pull request restructures and simplifies the adapter definitions by moving canonical sources under a new adapters/source/ directory, updating documentation, and removing redundant or generated files from tool-specific adapter directories. The changes clarify the contributor workflow and eliminate duplication, ensuring that only source files are committed and generated files are handled via build scripts.

Documentation and Structure Updates:

• Updated adapters/README.md to document the new canonical source layout under adapters/source/, describe the build process for generating adapter packs, and clarify the contributor workflow.

Removal of Redundant or Generated Files:

• Removed tool-specific capabilities.yaml files from adapters/claude-code/, adapters/codex/, adapters/generic/, and adapters/opencode/ as these are now generated from canonical sources. [1] [2] [3] [4]
• Deleted flow documentation markdown files (e.g., change-new.md, change-shape.md, promote.md, standard-discover.md) from all tool adapter directories, consolidating flow definitions in the canonical source. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15]

[Copilot]

Pull request overview

This PR advances the repo to 0.1.0-alpha.14 by adding new change-workflow capabilities (assessment, decomposition planning/apply, reciprocal related-change edits) and standard authoring commands, plus updating adapter flow docs/host-native artifacts and regenerating release/CLI reference fixtures to reflect the expanded CLI surface.

Changes:

• Add new runectx change advisory flows (assess-intake, assess-decomposition) and decomposition flows (decomposition-plan, decomposition-apply), including parsing, outputs/explain, metadata, and tests.
• Add runectx standard list|create|update contract + CLI support (with transactional writes) and tests.
• Update adapter flow documentation + host-native sync/render logic and bump alpha version + regenerate golden/reference fixtures.

Reviewed changes

Copilot reviewed 84 out of 85 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
runecontext/changes/CHG-2026-025-7854-migrate-assurance-artifacts-under-runecontext-for-alpha13-upgrades/status.yaml	Marks change as closed/passed and sets closed_at/promotion status.
runecontext/changes/CHG-2026-024-3756-plan-interval-based-real-migration-edge-discovery-for-project-upgrades/status.yaml	Marks change as closed/passed and sets closed_at/promotion status.
runecontext/changes/CHG-2026-006-5aaf-add-first-class-standard-authoring-commands/status.yaml	Moves status from proposed → implemented.
runecontext/changes/CHG-2026-005-d9ca-add-structured-change-update-command-for-safe-status-and-relationship-edits/status.yaml	Moves status from proposed → implemented.
runecontext/changes/CHG-2026-004-5b03-add-first-class-change-decomposition-planning-and-apply-operations/status.yaml	Moves status from proposed → implemented.
runecontext/changes/CHG-2026-003-5f38-teach-adapters-to-run-guided-clarification-and-decomposition-flows/status.yaml	Moves status from proposed → implemented.
runecontext/changes/CHG-2026-002-5739-add-guided-adapter-native-change-workflows/status.yaml	Moves status from proposed → implemented.
runecontext/changes/CHG-2026-001-fdc1-add-advisory-intake-and-decomposition-assessment-commands/status.yaml	Moves status from proposed → implemented.
runecontext/assurance/receipts/changes/changes--changes-ddcbd9ab-1774990654-dac1daf17ec2-bd66e6912b32.json	Adds verified receipt for CHG-2026-025 closure/verification.
runecontext/assurance/receipts/changes/changes--changes-257ebe76-1774990635-750948eb2860-4418558df4a8.json	Adds verified receipt for CHG-2026-024 closure/verification.
nix/release/metadata.nix	Bumps release version to 0.1.0-alpha.14.
internal/contracts/standard_commands_update.go	Implements standard update (frontmatter mutations + validated transactional rewrite).
internal/contracts/standard_commands_types.go	Adds standard list/create/update option/result structs + frontmatter type.
internal/contracts/standard_commands_test.go	Adds contract-level tests for standard list/create/update behavior.
internal/contracts/standard_commands_list.go	Adds standards listing with scope/focus/status filters.
internal/contracts/standard_commands_helpers.go	Adds standard path normalization, validation helpers, YAML rendering utilities.
internal/contracts/standard_commands_create.go	Implements standard create (validated transactional write).
internal/contracts/change_update.go	Adds related-change editing support and includes related changes in results.
internal/contracts/change_update_relationships.go	Adds relationship edit normalization + reciprocal write generation helpers.
internal/contracts/change_decomposition.go	Adds decomposition plan/apply operations and status rewrite generation.
internal/contracts/change_commands.go	Extends contracts with assessment + decomposition option/result types and related changes on results.
internal/contracts/change_commands_update_test.go	Adds tests for reciprocal related-change edits and edit conflict validation.
internal/contracts/change_assessment.go	Adds intake and decomposition advisory assessment logic.
internal/contracts/change_assessment_test.go	Adds tests for advisory assessment + decomposition plan/apply flows.
internal/cli/cli.go	Updates usage strings/examples and standard/change command summaries.
internal/cli/cli_upgrade_adapter_plans.go	Adjusts managed-host-native scan behavior during upgrade planning.
internal/cli/cli_standard.go	Adds standard subcommands and enables machine --dry-run at standard root.
internal/cli/cli_standard_update.go	Adds CLI wiring for standard update.
internal/cli/cli_standard_list.go	Adds CLI wiring for standard list + structured output.
internal/cli/cli_standard_create.go	Adds CLI wiring for standard create.
internal/cli/cli_standard_authoring_test.go	Adds CLI tests covering standard list/create/update and dry-run.
internal/cli/cli_standard_authoring_shared.go	Adds shared helpers/constants for standard authoring CLI output/explain.
internal/cli/cli_parse.go	Extends request structs and factors parsing into dedicated files.
internal/cli/cli_parse_change_update.go	Adds change update parsing for related-change flags.
internal/cli/cli_parse_change_decomposition.go	Adds parsing for --sub-change and --depends-on edges.
internal/cli/cli_parse_change_assess.go	Adds parsing for change assessment commands.
internal/cli/cli_metadata_registry.go	Registers new change/standard commands and switches standard to write machine flags.
internal/cli/cli_metadata_registry_test.go	Adds registry tests for new change decomposition/assessment commands + relationship flags.
internal/cli/cli_metadata_registry_adapter.go	Updates adapter render-host-native operation enum list.
internal/cli/cli_metadata_flags.go	Adds metadata for new flags (assessment/decomposition/standard + relationship edits).
internal/cli/cli_help_validate_flags_test.go	Updates help output test to include decomposition-apply example.
internal/cli/cli_explain.go	Adds explain output for new commands and related-change details.
internal/cli/cli_completion_test.go	Extends completion enum parity tests for assessment flags.
internal/cli/cli_completion_suggest_test.go	Refactors provider assertions and adds new provider expectations.
internal/cli/cli_change.go	Routes new change subcommands and passes related-change edits into contracts.
internal/cli/cli_change_update_relationship_test.go	Adds CLI-level tests for reciprocal relationship edit persistence + usage errors.
internal/cli/cli_change_test.go	Adds CLI tests for assess-intake and assess-decomposition behavior and usage errors.
internal/cli/cli_change_test_helpers_test.go	Moves shared CLI change test helpers into a dedicated file.
internal/cli/cli_change_output.go	Adds structured output for new commands and includes related changes in change update output.
internal/cli/cli_change_decomposition_test.go	Adds CLI tests for terminal-state behavior differences between plan vs apply.
internal/cli/cli_change_decomposition_flow_test.go	Adds end-to-end CLI tests for decomposition plan/apply outputs and dry-run behavior.
internal/cli/cli_change_advisory_decomposition.go	Implements CLI handlers for assess and decomposition commands.
internal/cli/cli_adapter_test.go	Updates adapter sync expectations for newly added host-native artifacts and refactors helpers.
internal/cli/cli_adapter_test_helpers_test.go	Extracts adapter test helpers (marker checks, hook scripts, permissions).
internal/cli/cli_adapter_sync_host_native.go	Switches to new flow mapping source and uses flow→command-path helper.
internal/cli/cli_adapter_sync_host_native_flows.go	Adds tool flow mappings including the new assessment/decomposition flows.
internal/cli/cli_adapter_render_test.go	Adds render-host-native tests for new operations and index contents.
internal/cli/cli_adapter_render_host_native_markdown.go	Adds flow ID → command path mapping for new hyphenated change commands.
internal/cli/cli_adapter_pack_test.go	Updates adapter pack required flows/mappings to include new flows.
fixtures/release/release-manifest-with-metadata.json	Updates manifest command list + version compatibility to alpha.14.
fixtures/cli-json-golden/metadata-success.json	Updates metadata golden output for new commands + alpha.14.
fixtures/cli-completion/zsh.golden	Updates zsh completion golden for new commands/flags/suggestions.
fixtures/cli-completion/fish.golden	Updates fish completion golden for new commands/flags/suggestions.
fixtures/cli-completion/bash.golden	Updates bash completion golden for new commands/flags/suggestions.
docs/reference/generated/runecontext-reference.json	Updates generated reference for alpha.14 + expanded command set.
adapters/opencode/flows/conversational-parity.md	Adds parity mappings for the 4 new conversational flows.
adapters/opencode/flows/change-decomposition-plan.md	Adds OpenCode flow documentation for decomposition planning.
adapters/opencode/flows/change-decomposition-apply.md	Adds OpenCode flow documentation for decomposition apply.
adapters/opencode/flows/change-assess-intake.md	Adds OpenCode flow documentation for intake assessment.
adapters/opencode/flows/change-assess-decomposition.md	Adds OpenCode flow documentation for decomposition assessment.
adapters/generic/flows/conversational-parity.md	Adds parity mappings for the 4 new conversational flows.
adapters/generic/flows/change-decomposition-plan.md	Adds generic flow documentation for decomposition planning.
adapters/generic/flows/change-decomposition-apply.md	Adds generic flow documentation for decomposition apply.
adapters/generic/flows/change-assess-intake.md	Adds generic flow documentation for intake assessment.
adapters/generic/flows/change-assess-decomposition.md	Adds generic flow documentation for decomposition assessment.
adapters/codex/flows/conversational-parity.md	Adds parity mappings for the 4 new conversational flows.
adapters/codex/flows/change-decomposition-plan.md	Adds Codex flow documentation for decomposition planning.
adapters/codex/flows/change-decomposition-apply.md	Adds Codex flow documentation for decomposition apply.
adapters/codex/flows/change-assess-intake.md	Adds Codex flow documentation for intake assessment.
adapters/codex/flows/change-assess-decomposition.md	Adds Codex flow documentation for decomposition assessment.
adapters/claude-code/flows/conversational-parity.md	Adds parity mappings for the 4 new conversational flows.
adapters/claude-code/flows/change-decomposition-plan.md	Adds Claude Code flow documentation for decomposition planning.
adapters/claude-code/flows/change-decomposition-apply.md	Adds Claude Code flow documentation for decomposition apply.
adapters/claude-code/flows/change-assess-intake.md	Adds Claude Code flow documentation for intake assessment.
adapters/claude-code/flows/change-assess-decomposition.md	Adds Claude Code flow documentation for decomposition assessment.

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Copilot reviewed 133 out of 146 changed files in this pull request and generated 9 comments.

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Copilot reviewed 154 out of 167 changed files in this pull request and generated 3 comments.

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