fix: filter trimmed module references

[atharvasingh7007]

Summary

• filter depends_on and depended_by to the retained module set when max_modules trims the graph
• drop dependency edges that point at trimmed modules
• compute most_depended and isolated from the retained modules so the generated index stays internally consistent
• add an engine regression test for a capped three-module graph

Root cause

assembleIndex() capped the modules map, but it still copied dependency metadata from the full graph. That could leave stacklit.json with dangling module references in modules.*.depends_on, modules.*.depended_by, dependencies.edges, and dependencies.most_depended.

Impact

With max_modules set below the full module count, Stacklit could emit an index where dependency edges point to modules that are no longer present in modules. That can mislead AI consumers and produce Mermaid edges to undefined nodes.

Validation

• gofmt -w internal/engine/engine.go internal/engine/engine_test.go
• go test ./...
• go build -o stacklit.exe ./cmd/stacklit
• ./stacklit.exe init