docs: OpenAPI and API.md cover every route; drop removed endpoints; guard config writes

- openapi-extra/run.js describes tmux pane runs only: the removed
  POST /api/run/{id}/message and stream-json run_stream/run_input_ack are gone.
- 108 operations added to OpenAPI (lanes, run, settings, reports, cc-config,
  pets, ai-proxies, tool-profiles, ai-tools, snapshots, locks, ...);
  openapi.yaml regenerated.
- docs/API.md: 74 routes added, 4 endpoints that no longer exist removed.
- Role is `developer`, not `member` (CLI.md, DATABASE.md, OVERVIEW.md);
  `agenthub update` -> `update-check`; help lists `server install-system|tools`
  and `users provision`; ARCHITECTURE.md's stale paths and names fixed.
- cc-config/codex-config writes carry sameOriginGuard (an MCP server or plugin
  is code Claude runs later), with a test; `command -v` takes its name as $1.

server/openapi-extra/cc-config.js

@@ -1903,6 +1903,65 @@ const paths = {
         },
       },
     },
+    patch: {
+      tags: ["CcConfig"],
+      summary: "Merge keys into one settings layer",
+      description:
+        'Sets and/or unsets dotted keys (`set: {"hooks.PreToolUse": [...]}`, `unset: ["model"]`) in one settings.json layer. The file is re-read unredacted and only the named keys change; a value containing the `<redacted>` placeholder is refused (`EREDACTED`). The project layers resolve against the SERVER\'s cwd, never `?cwd=`. An existing file is backed up first. Broadcasts `cc_config_changed`. Admin-only in server mode.',
+      operationId: "ccConfigPatchSettings",
+      requestBody: {
+        required: true,
+        content: {
+          "application/json": {
+            schema: {
+              type: "object",
+              required: ["scope"],
+              properties: {
+                scope: { type: "string", enum: ["user", "project", "project-local"] },
+                set: { type: "object", additionalProperties: true },
+                unset: { type: "array", items: { type: "string" } },
+              },
+            },
+          },
+        },
+      },
+      responses: {
+        200: {
+          description: "Written (or nothing changed).",
+          content: {
+            "application/json": {
+              schema: {
+                type: "object",
+                properties: {
+                  path: { type: "string" },
+                  backupPath: { type: "string", nullable: true },
+                  created: { type: "boolean" },
+                  changed: { type: "array", items: { type: "string" } },
+                },
+              },
+            },
+          },
+        },
+        400: {
+          description: "`EBADSCOPE`, `EBADCONTENT` (nothing to change) or `EREDACTED`.",
+          content: {
+            "application/json": { schema: { $ref: "#/components/schemas/ErrorResponse" } },
+          },
+        },
+        409: {
+          description: "`EBADJSON` — the file on disk is not a JSON object; fix it by hand.",
+          content: {
+            "application/json": { schema: { $ref: "#/components/schemas/ErrorResponse" } },
+          },
+        },
+        413: {
+          description: "`ETOOLARGE`.",
+          content: {
+            "application/json": { schema: { $ref: "#/components/schemas/ErrorResponse" } },
+          },
+        },
+      },
+    },
   },
 
   "/api/cc-config/memory": {