task: Architecture — workspaces, cross-repo, worktrees, benchmarks (6 issues)

[DeusData]

Scope

Umbrella tracker for larger feature requests / architectural proposals that don't map to a single bug. Each item here typically needs a small design discussion before implementation.

Sub-issues

• Cross-crate call graphs stop at boundaries #56 — Cross-crate call graphs stop at boundaries (Rust workspaces)
• Workspace support: package.json#workspaces, pnpm-workspace.yaml, and [workspace] in Cargo.toml — proposal #271 — Workspace support: package.json#workspaces, pnpm-workspace.yaml, [workspace] in Cargo.toml — proposal
• Feature Request: Automatic deletion of project when underlying folder is deleted #286 — Feature Request: Automatic deletion of project when underlying folder is deleted
• Protocol-aware cross-repo intelligence: gRPC + typed-message + attribute-route matching (design proposal) #292 — Protocol-aware cross-repo intelligence: gRPC + typed-message + attribute-route matching (design proposal)
• Support efficient indexing for Git worktree-based agent development workflows #351 — Support efficient indexing for Git worktree-based agent development workflows
• Add new benchmark with memtrace-public #356 — Add new benchmark with memtrace-public

PR #369 (workspace imports + SvelteKit filesystem routes) is a partial implementation of #271 / #56's TypeScript-monorepo half — please review there before scoping further.

Acceptance

Per item:

1. A short design note (or rejection with rationale) in this issue or a sub-issue.
2. If in scope: implementation tracked in its own follow-up issue or PR.

Why one task

These are not bugs — they're feature/architecture asks. Triaging them together prevents them from drifting into the backlog uncategorized.

Added 2026-06-24 (triage)

• package.json workspaces cross-repo IMPORTS still produce zero edges (v0.7.0 follow-up to #308) #408 — package.json workspaces cross-repo IMPORTS still produce zero edges (relates Workspace support: package.json#workspaces, pnpm-workspace.yaml, and [workspace] in Cargo.toml — proposal #271)
• Architectural Drift Detection Between Git Revisions #525 — Architectural Drift Detection between git revisions
• feat: SwiftPM package-graph support (Package.swift manifest resolution) for cross-package/cross-repo edges #551 — SwiftPM package-graph support (Package.swift manifest resolution)
• New MCP tool to manage cross-service links #561 — New MCP tool to manage cross-service links (relates Protocol-aware cross-repo intelligence: gRPC + typed-message + attribute-route matching (design proposal) #292)
• Feature request: worktree overlay indexing for branch-aware agent workflows #573 — worktree overlay indexing for branch-aware agent workflows (relates feat(git): add worktree branch roots #401 / Feature Request: Automatic deletion of project when underlying folder is deleted #286)

ADR / MADR

• Support Markdown Architectural Decision Records #507 — Support Markdown Architectural Decision Records (MADR)
• Make the tool import existing ADR docs in a repository #504 — Import existing ADR docs (duplicate of Support Markdown Architectural Decision Records #507)
• manage_adr data loss: ADRs in project_summaries are deleted during graph re-indexing #516 — manage_adr data loss during re-index — tracked via PR fix(pipeline): preserve ADR across full re-index (#516)fix(pipeline): preserve ADR across full re-index (#516) #539

Added 2026-06-29 (triage)

Worktrees and git-root behavior

• fix(detect_changes): impacted_symbols always empty for projects inside git worktrees #690 — detect_changes worktree implementation tracker (relates detect_changes: impacted_symbols always empty for projects inside git worktrees (canonical_root miscalculated) #659)
• fix(git): index_repository ignores .git/info/exclude and core.excludesFile inside linked git worktrees #689 — linked-worktree git excludes implementation tracker (relates index_repository ignores .git/info/exclude and core.excludesFile inside linked git worktrees #682)
• index_repository ignores .git/info/exclude and core.excludesFile inside linked git worktrees #682 — index_repository ignores .git/info/exclude and core.excludesFile in linked worktrees
• detect_changes: impacted_symbols always empty for projects inside git worktrees (canonical_root miscalculated) #659 — detect_changes.impacted_symbols empty for projects inside git worktrees

Cross-repo / protocol architecture

• Go services get 0 cross-repo edges (Fiber route paths empty, gRPC not captured) #686 — Go Fiber route paths empty, gRPC not captured, Kafka noted as Tier 2
• cross-repo-intelligence: 0 edges for FastAPI backend — Route.path empty, router prefix stripped #678 — FastAPI route path / router-prefix extraction blocks cross-repo HTTP edges
• feat(pipeline): NATS subject detection for cross-repo ASYNC_CALLS edges (Tier 2 follow-up to #292) #652 — NATS subject detection for cross-repo async edges
• implement ingest_traces — create CROSS_* edges from runtime traces (currently a no-op stub) #612 — ingest_traces runtime trace ingestion for CROSS_* edges
• Feature request: Execution flow / process abstraction for high-level code comprehension #597 — execution-flow / process abstraction for high-level comprehension
• cross-repo-intelligence returns 0 edges for a byte-identical call/route #523 — cross-repo-intelligence returns zero edges for byte-identical call/route
• Add cross-repo Maven library dependency links #440 — cross-repo Maven dependency links

Added 2026-06-30 (triage)

• cross-repo HTTP edges missing when caller URL is a constant #706 — cross-repo HTTP edge creation misses centralized URL constants / partial URL matching

[sahil-mangla]

@DeusData I will give it a shot by first creating a design note for it :)