Refine dev.kit repo context and agent flow

[fqjony]

Changes

• add dev.kit env plus env config controls so repo and agent output reflect actual tool and credential availability
• improve manifest evidence tracing from top-level version headers, repo-owned GitHub references, and real usage paths
• collapse manifest evidence into cleaner dependency output, filter placeholder GitHub refs like org/repo, and avoid false repo traces from nested content version fields
• keep dev.kit repo --json backward-compatible by retaining profile: null while the new contract centers on archetype
• remove dev.kit learn from the public command surface and trim related configs, templates, and docs
• add upgrade-first guidance to generated AGENTS.md and install docs
• keep fixture coverage minimal and add an optional local tests/real-repos.sh runner for broader repo trials

Verification

• make test
• local bash tests/real-repos.sh ... smoke checks

[Copilot]

Pull request overview

This PR refactors dev.kit toward a tighter “env → repo context → agent guidance” loop by (1) making repo context generation more traceable/structured (refs/commands/gaps/deps/manifests) and (2) simplifying the public surface area and test fixtures to focus on core flows and real-repo trials.

Changes:

• Add dev.kit env + an env config file format for disabling tools/credentials, and update the default dev.kit home command to sync .rabbit/context.yaml + AGENTS.md.
• Rework detection/config catalogs (archetypes, signals, patterns, context sections) and dependency/manifest tracing to be more evidence-driven.
• Reduce/remove “learn” and several fixture/config catalogs; replace broader fixture coverage with optional real-repo and worker-image smoke runners.

Reviewed changes

Copilot reviewed 66 out of 68 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/worker-smoke.sh	New docker-based smoke runner that installs dev.kit into the worker image and runs dev.kit* commands.
tests/suite.sh	Shrinks suite to a minimal “core” flow and updates assertions to match new outputs/artifacts.
tests/real-repos.sh	New opt-in local script to run dev.kit against real local repos without global install changes.
tests/local-udx.sh	Removed local UDX-only repo scanner in favor of more generic real-repo runner.
tests/fixtures/workflow-repo/README.md	Removed fixture content as part of fixture minimization.
tests/fixtures/workflow-repo/.github/workflows/reusable-check.yml	Removed workflow fixture as part of fixture minimization.
tests/fixtures/wordpress-repo/wp-content/mu-plugins/bootstrap.php	Removed WordPress fixture file.
tests/fixtures/wordpress-repo/wp-config.php	Removed WordPress fixture file.
tests/fixtures/wordpress-repo/README.md	Removed WordPress fixture doc.
tests/fixtures/wordpress-repo/package.json	Removed WordPress fixture manifest.
tests/fixtures/wordpress-repo/.rabbit/infra_configs/development/develop-alex/aws-cloudfront-distribution.yaml	Removed WordPress infra fixture.
tests/fixtures/wordpress-repo/.rabbit/infra_configs/development/aws-cloudfront-distribution.yaml	Removed WordPress infra fixture.
tests/fixtures/wordpress-repo/.github/workflows/deploy.yml	Removed WordPress workflow fixture.
tests/fixtures/php-repo/tests/ExampleTest.php	Removed PHP fixture.
tests/fixtures/php-repo/phpunit.xml	Removed PHP fixture.
tests/fixtures/php-repo/composer.json	Removed PHP fixture.
tests/fixtures/codex-home/sessions/2026/04/02/rollout-2026-04-02T20-54-19-019d4f54-eddc-7350-a757-3bb578d24f99.jsonl	Removed codex fixture session data.
src/templates/repo.json	Updates repo --json template (drops profile).
src/templates/learn.json	Removed learn JSON template.
src/templates/agent.json	Updates agent --json template (drops profile).
src/configs/repo-scaffold.yaml	Removed scaffold config catalog.
src/configs/learning-workflows.yaml	Removed learn workflow config catalog.
src/configs/knowledge-base.yaml	Removed knowledge-base config catalog.
src/configs/github-prs.yaml	Removed GitHub PR guidance catalog.
src/configs/github-issues.yaml	Removed GitHub issue guidance catalog.
src/configs/development-workflows.yaml	Removed development workflow catalog (moves toward repo-derived workflow steps).
src/configs/development-practices.yaml	Removed practices catalog (moves away from inlined practice rules).
src/configs/detection-signals.yaml	Refines factor/dependency/manifest detection signals and lists.
src/configs/detection-patterns.yaml	Refines regex patterns; adds YAML kind/apiVersion patterns.
src/configs/context-config.yaml	Introduces context section schemas + ref prioritization/glob support.
src/configs/audit-rules.yaml	Updates gap messages; adds descriptions/metadata.
src/configs/archetypes.yaml	Renames/reshapes archetype rules and matching facets.
src/configs/archetype-signals.yaml	Removed separate archetype signal file (merged into detection signals).
README.md	Rewrites README for upgrade-first guidance + new command roles + test entrypoints.
README_old.md	Adds previous README content as an “old” reference.
Makefile	Adds test-real target for optional real-repo checks.
lib/modules/utils.sh	Removes unused YAML scalar helper.
lib/modules/repo_workflows.sh	Adds entrypoint source helper; removes learn step from workflow steps.
lib/modules/repo_signals.sh	Improves glob handling, documented command extraction + source tracking, and adds Next/CLI signals.
lib/modules/repo_reports.sh	Updates agent contract text to be context-first.
lib/modules/repo_factors.sh	Refactors command detection to return command + source; adjusts config-factor evidence.
lib/modules/repo_archetypes.sh	Refactors facets/archetype inference (Next, YAML manifest detection, K8s detection tightening).
lib/modules/output.sh	Removes output hint helper.
lib/modules/local_env.sh	Adds env config read/ensure logic; implements disable-by-config behavior for tools/credentials.
lib/modules/dev_sync.sh	Inlines branch role/base branch defaults (removes dependency on removed workflow config).
lib/modules/config_catalog.sh	Removes learn/practices/workflow config cataloging; adds context section helpers and ref glob expansion.
lib/modules/bootstrap.sh	Removes learn from public commands and module path list.
lib/commands/repo.sh	Switches repo mode naming to “write” and adjusts next-step messaging.
lib/commands/learn.sh	Removes the learn command implementation.
lib/commands/env.sh	Adds new env command implementation.
lib/commands/agent.sh	Simplifies generated AGENTS.md content; removes learn/GitHub-history/practices integration.
docs/smart-dependency-detection.md	New doc describing deterministic dependency tracing behavior.
docs/integration.md	Removed integration doc (replaced by newer docs structure).
docs/installation.md	Adds upgrade-first guidance and positions dev.kit as the happy-path entrypoint.
docs/how-it-works.md	New doc describing command flow and regeneration model.
docs/experience-guidance.md	New doc describing what AGENTS.md should/shouldn’t do.
docs/environment-config.md	New doc describing env detection + env config controls.
docs/context.md	Removed old context doc (replaced by context-coverage/how-it-works).
docs/context-coverage.md	New doc describing what context.yaml should cover and how to repair gaps.
docs/agents.md	Removed old agents doc (replaced by experience-guidance/how-it-works).
config/env.yaml	Adds a repo-checked example env config file.
bin/dev-kit	Updates CLI usage, adds syncing behavior on dev.kit, and wires up env command help.
AGENTS.md	Updates generated artifact in-repo to new guidance shape.
.rabbit/context.yaml	Updates generated context example to new structured sections (commands/gaps/deps/manifests).

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