Atlas 0.4.1: exact path explorer and complete infrastructure intelligence

[Shahinyanm]

What this completes

This PR finishes the remaining Atlas 0.4 plan after #32 was merged and prepares the publishable 0.4.1 release.

Exact architecture paths

• adds indexed shortest-path search between any two exact graph nodes
• adds the atlas_find_path MCP tool
• adds a visual Path A -> B workflow with start/target picking, directed and any-connection modes
• renders only the exact numbered chain and preserves truthful arrow direction
• adds clear no-path and safety-limit states

Infrastructure intelligence

• reusable GitHub Actions workflows and action dependencies
• richer CI job metadata
• Docker Compose health checks, networks, volumes, configs, secrets, and env-file links
• Kubernetes init containers, volume mounts, autoscaling, workload policy metadata
• Kustomize image overrides, Helm chart/value metadata, and Argo CD applications
• cache schema bump so existing projects are rescanned after upgrade
• secret values remain excluded; only names and safe structure are retained

System Map correction

• preserves aggregate arrows connected to visible domain groups in the default Clusters view
• adds Delivery & Runtime directly to System Map, including CI/CD, images, workloads, networking and environments
• keeps operations edges in the map data instead of collapsing them into generic domains
• hovering a component isolates its direct system-level connections
• adds regression tests so level-of-detail optimization cannot remove grouped connections again

Large-project UX

• indexed right-panel incoming/outgoing links
• indexed flow membership, table counts, migration operations, and configuration consumers
• bounded path search and queue traversal without repeated array shifting
• Architecture hubs on Overview
• expanded tests and public documentation

Graphify review

Atlas adopts the useful query-first ideas: exact graph paths, architecture hubs, evidence/confidence visibility, and bounded large-graph behavior. It keeps Atlas's directed, NestJS-specific semantic graph and deterministic scenes instead of replacing them with an undifferentiated generic network.

Release

• package version: 0.4.1
• no project-specific paths or pl-api data
• existing scan cache is invalidated by the analyzer schema bump

Verification

CI runs the complete check on Linux, macOS, and Windows:

• lint
• typecheck
• full tests
• production website build

The test suite covers 19 MCP tools, infrastructure fixtures, viewer path interaction, and large-graph path performance.