feat: add --prompt flag to run start

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ellipsis/cli",
-  "version": "0.1.3",
+  "version": "0.1.4",
   "description": "Ellipsis agent CLI — drive the Ellipsis cloud from your terminal",
   "license": "MIT",
   "type": "module",

src/commands/run.tsx

@@ -52,6 +52,10 @@ export function registerRun(program: Command): void {
       '-o, --config-override <yaml>',
       'partial agent config (YAML) merged onto the chosen config for this run, e.g. "limits:\\n  run: 5"',
     )
+    .option(
+      '-p, --prompt <text>',
+      'per-run instructions appended to the initial user query for this run',
+    )
     .option(
       '-m, --metadata <key=value>',
       'attach metadata (repeatable)',
@@ -67,6 +71,7 @@ export function registerRun(program: Command): void {
         configFile?: string
         template?: string
         configOverride?: string
+        prompt?: string
         metadata: Record<string, string>
         source: string
         watch?: boolean
@@ -92,6 +97,9 @@ export function registerRun(program: Command): void {
           // Merged onto the chosen config and re-validated server-side; set
           // limits.run here to override this run's budget.
           if (opts.configOverride) req.config_override_yaml = opts.configOverride
+          // Appended to the initial user query at build time; gives this run
+          // instructions on top of the config's shared system prompt.
+          if (opts.prompt) req.prompt = opts.prompt
 
           const api = new ApiClient()
           const run = await api.startAgentRun(req)

src/lib/types.ts

@@ -136,6 +136,10 @@ export interface StartAgentRunRequest {
   // server-side, e.g. "limits:\n  run: 5.0" to set just this run's budget. Only
   // meaningful with config_id/template_id.
   config_override_yaml?: string
+  // Per-run instructions appended to the initial user query at build time, after
+  // the config's shared `claude.system` system prompt. Distinct from the system
+  // prompt, which is identical for every run of a config.
+  prompt?: string
 }
 
 export interface ListAgentRunsResponse {