docs: v2.93 GAP-MATRIX resolution — root docs refresh, changelog format count fix

CURRENT_STATUS.md bumped to v2.93 with GAP-MATRIX-07/01b/02 changelog entry.
Test count 7,654. CHANGELOG.md wire format count 4→5.

Made-with: Cursor

Author: eastgate

CHANGELOG.md

@@ -159,7 +159,7 @@ All notable changes to biomeOS will be documented in this file.
 - `rescan_primals()` resets lazy flag for subsequent misses
 
 ### BM-05: Probe Response Format (RESOLVED)
-- `extract_capabilities_from_response()` in `cap_probe.rs` handles 4 wire formats (string array, object array with `name`, top-level array, `methods` key)
+- `extract_capabilities_from_response()` in `cap_probe.rs` handles 5 wire formats (A: flat string array, B: object array, C: method_info, D: semantic_mappings, E: provided_capabilities)
 - Unrecognized formats logged at `warn!` level (not `debug!`)
 - Probe timeout centralized to `timeouts::PROBE_TIMEOUT` constant
 

CURRENT_STATUS.md

@@ -1,7 +1,7 @@
 # biomeOS - Current Status
 
-**Updated**: April 7, 2026 (v2.92: deep debt evolution — probe_endpoint stub→real JSON-RPC, tokio-tungstenite 0.21→0.24 aligned with axum, tokio test-util→dev-deps in 5 crates, nucleus.rs hardcoding→capability-based dispatch, detect_ecosystem→dynamic socket scan, abstract socket dedup, root detection bug fixed in genome_deploy, "registry" taxonomy alias added)
-**Version**: 2.92
+**Updated**: April 7, 2026 (v2.93: GAP-MATRIX resolution — GAP-07 critical proxy forwarding fixed (unix:// URI scheme in TransportEndpoint::parse), GAP-01b Format E capability parser for BearDog provided_capabilities wire format, GAP-02 DeploymentGraph name/version made optional for TOML tolerance)
+**Version**: 2.93
 **Status**: PRODUCTION READY - Capability-Based Discovery Compliant - Zero Blocking Debt - Fully Concurrent Testing
 
 ---
@@ -17,7 +17,7 @@
 | **Security Score** | 100/100 (HSTS, X-Frame, CSP, Referrer-Policy, Cache-Control) |
 | **Code Quality** | A++ (Pure Rust, Edition 2024 all crates, ecoBin v3.0, fully concurrent, zero warnings, full doc coverage, sovereignty audit) |
 | **Lint hardening** | `deny` on unwrap_used/expect_used, workspace lints inherited by all 26 workspace crates |
-| **Tests Passing** | 7,649 lib + bin + doc + proptest (0 failures, 0 ignored, fully concurrent) |
+| **Tests Passing** | 7,654 lib + bin + doc + proptest (0 failures, 0 ignored, fully concurrent) |
 | **Test Coverage** | 90%+ region / function / line (llvm-cov workspace-wide, target maintained) |
 | **Unsafe Code** | 0 production (`#[forbid(unsafe_code)]` on all crate roots, `mem::forget` eliminated) |
 | **Clippy** | PASS (0 warnings, pedantic+nursery, `-D warnings`, all crates via `[lints] workspace = true`) |
@@ -34,6 +34,8 @@
 | **Discovery Model** | 5-tier capability-first protocol (centralized) + taxonomy + manifest fallback |
 | **NAT Traversal** | 4-tier strategy (LAN/punch/coordinated/relay) |
 | **P2P Sovereign Onion** | PRODUCTION READY |
+| **GAP-MATRIX Resolution v2.93 (Apr 7)** | **GAP-MATRIX-07 (Critical):** `TransportEndpoint::parse()` now handles `unix://` URI scheme. Previously, `display_string()` round-trips and external `capability.register` calls with `unix:///path` strings were misrouted to TCP parsing, creating broken `PathBuf` values. All `capability.call` forwarding through discovered endpoints now works end-to-end. **GAP-MATRIX-01b (Medium):** Added Format E to 5-format capability parser: `result.provided_capabilities: [{type: "security", methods: ["sign", ...]}]` (BearDog wire format). Emits both group type ("security") and qualified methods ("security.sign"). Both `cap_probe.rs` canonical + `ai_advisor.rs` mirror updated. BearDog's 9 capability groups now register correctly. **GAP-MATRIX-02 (Medium):** `GraphDefinition.name` and `.version` now `#[serde(default)]`, matching `neural_graph::Graph` parser. `tower_atomic_bootstrap.toml` (which omits name/version) now parses through both `DeploymentGraph` and `neural_graph` code paths. 5 new tests, 7,654 total (0 failures), clippy PASS. |
+| **Deep Debt Evolution v2.92 (Apr 7)** | probe_endpoint stub→real JSON-RPC liveness probes (identity.get + capabilities.list over Unix sockets), 4-format capability parser aligned across biomeOS and primalSpring, nucleus.rs hardcoded primal fallbacks→CapabilityTaxonomy-only resolution, detect_ecosystem hardcoded CORE_PRIMALS list→dynamic socket directory scan, Toadstool-specific health logic→convention-based (.jsonrpc.sock detection), tokio-tungstenite 0.21→0.24 (aligned with axum 0.7), tokio test-util→dev-deps in 5 production crates, templates.rs hardcoded /tmp fallback→SystemPaths-only, genome_deploy root detection bug fixed, atomic_client abstract socket dedup, "registry" added as CapabilityTaxonomy alias for Discovery→songbird. |
 | **Deep Debt Evolution v2.91 (Apr 6)** | (1) **4 large files smart-refactored**: `topology.rs` 869→433 (tests→`topology_tests.rs`), `rendezvous.rs` 862→321 (tests→`rendezvous_tests.rs`), `verify.rs` 859→500 (tests→`verify_tests.rs`), `orchestrator.rs` 855→427 (tests→`orchestrator_tests.rs`). (2) **27 new tests across 5 files**: `storage_tests.rs` (+6: VolumeType variants, VolumeProjection, VolumeSpec round-trip), `networking_services_tests.rs` (+6: MeshEgressSpec, VirtualService redirect/rewrite, GatewaySpec, TrafficPolicy, TlsRouteSpec), `topology_tests.rs` (+4: proprioception degraded, connections, get_primals, motor coordination), `capability_tests.rs` (+4: providers, discover, register_route, route+metrics), `lifecycle_tests.rs` (+7 new file: status, shutdown_all, resurrect/apoptosis validation, register+get, status count, default reason). (3) **Duplicate dep audit**: all 25 duplicate roots are transitive (thiserror v1←rtnetlink/tungstenite, rand v0.8←tarpc/tungstenite, itertools v0.10←criterion dev-dep). No action possible. (4) **Quality gates**: 7,638 tests (0 failures, 0 ignored), clippy PASS, fmt PASS. |
 | **primalSpring/wetSpring Gap Resolution v2.90 (Apr 6)** | **Gap 1 — Neural API Semantic Method Fallback (BLOCKS LIVE NUCLEUS):** Added universal semantic routing fallback to Neural API — any `domain.operation` JSON-RPC method not in `ROUTE_TABLE` now automatically routes through `capability.call` via `CapabilityTranslationRegistry`. Springs can call `provenance.begin`, `birdsong.decrypt`, `dag.dehydrate`, `composition.tower_health`, etc. as top-level JSON-RPC methods. Explicit table entries (graph.*, topology.*, health.*, mesh.*, etc.) take precedence. `MeshCapabilityCall` renamed to `SemanticCapabilityCall`. 5 new routing tests (semantic fallback for provenance, birdsong, dag, composition, multipart). **Gap 2 — RootPulse Graph Execution:** Added 32 new capability translations for provenance trio: **dag domain** (rhizoCrypt: dag.create_session/dehydrate/rehydrate/get_session/list_sessions/add_vertex/slice + session/dehydration aliases + provenance.begin/begin_session), **commit domain** (LoamSpine: commit.session/append/get/list + permanent_storage/spine aliases), **attribution domain** (sweetGrass: provenance.create_braid/get_braid/verify + attribution/braid aliases). **birdsong.decrypt/encrypt** legacy aliases→BearDog beacon. Environment-driven providers: `BIOMEOS_DAG_PROVIDER`, `BIOMEOS_HISTORY_PROVIDER`, `BIOMEOS_ATTRIBUTION_PROVIDER`. RootPulse TOML workflows (`rootpulse_commit.toml` etc.) now resolve all `capability_call` nodes through translation registry. **Gap 3 — Composition Health Canonical Namespace:** Added `composition` domain to `CAPABILITY_DOMAINS` (biomeOS-local). 9 canonical composition health translations: `composition.health` (canonical), `composition.tower_health` (gen3), `composition.service_health`, `composition.science_health` (springs), `composition.webb_health`/`webb_compute_health`/`webb_storage_health`/`webb_network_health` (gen4), `composition.nucleus_health`. All normalize to `composition.health` on biomeOS-local. |
 | **Deep Debt Evolution v2.89 (Apr 6)** | (1) **Workspace dep governance finalized**: 22 remaining local dep pins→2 (only `biomeos-genomebin-v3` v3.0.0 and `biomeos-genome-factory` v1.0.0 retain local versions as intentional publishing versions). `biomeos-ui` workspace metadata aligned (`version.workspace`, `authors.workspace`, `license.workspace`, `rust-version.workspace`, external deps `{ workspace = true }`). (2) **2 large files smart-refactored**: `socket_providers.rs` 884→484 LOC (tests→`socket_providers_tests.rs`), `protocol.rs` 878→448 LOC (tests merged into existing `protocol_tests.rs`). (3) **Targeted test coverage for 5 untested production files**: `health.rs` (serde round-trips, HealthCheckTarget variants, MetricThreshold, HealthCheckConfig, issues), `service/core.rs` (ServiceStatus, ServiceSpec, ReplicaStatus serde), `definition.rs` (representative_for_category, resolve_to_primal, from_str_flexible, domain checks), `ai_advisor.rs` (GraphSnapshot, parallelization, DAG suggestions, learn_from_event, SuggestionFeedback serde), `fractal.rs` (Hybrid topology, N-ary branching, Leaf spawn_sub_node error). (4) **Library eprintln audit**: 3 occurrences verified — `or_exit.rs` (2, CLI fatal-exit pattern, tracing useless at `process::exit`), `capability_domains.rs` (1, test code). Zero actionable. (5) **Quality gates**: 7,607 tests (0 failures, 0 ignored), clippy PASS, fmt PASS. |