docs: align prose with multi-file server layout

README, HUMANS, and mcp-tools now describe implementation as src/server/ plus entry server.ts instead of implying a single monolithic file.

Author: AlbinoGeek

HUMANS.md

@@ -2,7 +2,7 @@
 
 Read-only MCP git tools for any workspace. **How the server is installed and wired to clients:** **[docs/install.md](docs/install.md)** only (do not restate that material here).
 
-**Implementation maps, `src/server.ts` symbols, and contract bumps** live in **`AGENTS.md`** at the repository root. This guide does not repeat those sections.
+**Implementation map (modules under `src/server/`, entry `src/server.ts`), symbols, and contract bumps** live in **`AGENTS.md`** at the repository root. This guide does not repeat those sections.
 
 **Registered tool ids, client naming (`rethunk-git_*`), `format` / JSON envelopes, resource URI, workspace root resolution:** **[docs/mcp-tools.md](docs/mcp-tools.md)** — canonical; not duplicated here.
 

README.md

@@ -11,6 +11,6 @@ Read-only **git** tools over MCP (status, multi-root inventory, `HEAD` parity, p
 | **[docs/install.md](docs/install.md)** | Single source for prerequisites, running the package, and every supported MCP client (plus from-source and troubleshooting) |
 | **[docs/mcp-tools.md](docs/mcp-tools.md)** | Tool ids, client naming, `format` / JSON, resource URI, workspace root resolution (canonical reference) |
 | **[HUMANS.md](HUMANS.md)** | Preset file, dev commands, CI, publishing |
-| **[AGENTS.md](AGENTS.md)** | Contributors: [`src/server.ts`](src/server.ts) map, contract bumps, CI (IDEs that inject this file as project context should not re-link it from rules) |
+| **[AGENTS.md](AGENTS.md)** | Contributors: implementation map ([`src/server/`](src/server/) + entry [`src/server.ts`](src/server.ts)), contract bumps, CI (IDEs that inject this file as project context should not re-link it from rules) |
 
 **Tools at a glance:** see the table in **[docs/mcp-tools.md](docs/mcp-tools.md)**.

docs/mcp-tools.md

@@ -1,7 +1,7 @@
 # MCP tools and resources (canonical reference)
 
 Single source of truth for **registered tool ids**, **client naming**, **JSON output shape**, **resource URI**, and **workspace root resolution**.  
-**Install and MCP clients (only canonical location):** [install.md](install.md). **Preset file, dev, CI, publishing:** [HUMANS.md](../HUMANS.md). **Implementation (`src/server.ts`), contract bumps:** [AGENTS.md](../AGENTS.md).
+**Install and MCP clients (only canonical location):** [install.md](install.md). **Preset file, dev, CI, publishing:** [HUMANS.md](../HUMANS.md). **Implementation layout (`src/server/` + entry [`server.ts`](../src/server.ts)), contract bumps:** [AGENTS.md](../AGENTS.md).
 
 ## Naming