Implement Sophia MVP scaffold (stages 0–3 + topology pivot)

Six-crate Rust workspace (core/sim/llm/store/server/bin) backing a
Three.js + WebGL frontend. Live at http://127.0.0.1:7777 via `cargo run`.

Sim
- Event-driven scheduler with min-heap, per-engram tick, staggered Spawn
  events (40 ms apart) so each engram's flight is visually readable.
- Solid-donut torus topology (replaces original spherical density-driven
  shell, see Topology Pivot in docs/system-analysis.md). Configurable
  major/minor radii in config.toml; live `POST /api/galaxy/:id/resize`.
- Physics: Verlet integration + friction; in-hole pull + galactic spin
  (CCW around +z) for spiral-ejection ejection from the donut centre;
  soft tube boundary with velocity-reflecting wall.
- Cosine-weighted gravity (kiddo k-NN within radius 25, threshold 0.50)
  and synapse formation (threshold 0.62) gated to inside-the-tube only.
- LM Studio integration via OpenAI-compatible REST: batched embeddings,
  optional Bearer auth, semaphore-bounded parallel ops per §13.5.

Server
- axum HTTP + WebSocket. Routes: /healthz, /api/galaxy CRUD, /seed,
  /ingest, /resize, /engrams/:id, /ws/galaxy/:id/events.
- Binary 12-byte-aligned position frames at ~20 Hz; JSON for sparse
  events (Hello, EngramCreated, SynapseCreated, TorusUpdated).
- Layered config: config.toml (defaults) + config.local.toml (secrets,
  gitignored) merged on startup.

Frontend
- Vite + vanilla TypeScript + three.js 0.169.
- Engrams render as additive bloom-friendly point sprites with a
  per-engram hash-driven hue rotation and breathing pulse.
- Comet-style velocity-aligned trails; additive ribbon synapses whose
  endpoints track engram positions every frame.
- UnrealBloomPass + ACES tone-mapping for the linked-particles look.
- HUD shows torus dims, engram + synapse counts, LM Studio status;
  controls for seed, ingest, and live torus resize.

Docs
- README replaced with docs/IDEA.md; system-analysis.md updated with
  the topology pivot decisions and Galaxy Ejection refinement notes
  (the implementation plan lives in ~/.claude/plans, gitignored).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Cargo.toml

@@ -0,0 +1,67 @@
+[workspace]
+resolver = "2"
+members = [
+    "crates/sophia-core",
+    "crates/sophia-sim",
+    "crates/sophia-llm",
+    "crates/sophia-store",
+    "crates/sophia-server",
+    "crates/sophia-bin",
+]
+
+[workspace.package]
+version = "0.0.1"
+edition = "2021"
+license = "MIT"
+rust-version = "1.80"
+authors = ["Sophia"]
+
+[workspace.dependencies]
+# Internal
+sophia-core   = { path = "crates/sophia-core" }
+sophia-sim    = { path = "crates/sophia-sim" }
+sophia-llm    = { path = "crates/sophia-llm" }
+sophia-store  = { path = "crates/sophia-store" }
+sophia-server = { path = "crates/sophia-server" }
+
+# Errors / runtime
+anyhow            = "1"
+thiserror         = "1"
+tokio             = { version = "1.40", features = ["full"] }
+async-trait       = "0.1"
+
+# Serde
+serde             = { version = "1", features = ["derive"] }
+serde_json        = "1"
+
+# Logging
+tracing            = "0.1"
+tracing-subscriber = { version = "0.3", features = ["env-filter", "fmt"] }
+
+# Math, ids
+glam              = { version = "0.28", features = ["serde"] }
+uuid              = { version = "1", features = ["v7", "serde"] }
+
+# HTTP/WS server (used by sophia-server only)
+axum              = { version = "0.7", features = ["ws", "macros"] }
+tower             = "0.5"
+tower-http        = { version = "0.6", features = ["fs", "trace", "cors"] }
+
+# HTTP client (LM Studio)
+reqwest           = { version = "0.12", features = ["json", "stream"] }
+
+# Sim
+kiddo             = "4"
+rand              = { version = "0.8", features = ["small_rng"] }
+
+# Async helpers
+futures-util      = { version = "0.3", default-features = false, features = ["std", "sink"] }
+bytes             = "1"
+
+# Config
+toml              = "0.8"
+
+[profile.release]
+lto       = "thin"
+codegen-units = 1
+opt-level = 3