fix: address PR #24 review feedback (spike options, flatten safety, MCP witness gate)

- cli-args.ts: parseSpikeArgs now rejects unrecognized --options
- doctor.ts: flatten repair only deletes the source .md file, removes
  dir only if empty (prevents data loss for dirs with extra files)
- mcp.ts: method_close now requires witnessVerified=true, matching
  the CLI's human-in-the-loop gate

Author: flyingrobots

docs/MCP.md

@@ -202,13 +202,15 @@ Check active cycle playback questions against tests
 
 ### `method_close`
 
-Close an active cycle into its retro packet.
+Close an active cycle into its retro packet. Requires witnessVerified=true to confirm human witness verification.
 
 **Parameters:**
 
 - `cycle` (optional) `string`
 - `driftCheck` (required) `boolean`
 - `outcome` (required) `string` (hill-met, partial, not-met)
+- `witnessVerified` (required) `boolean` — Human attestation that the witness and human playback questions have been verified.
+- `summary` (optional) `string` — Retro summary.
 
 ### `method_sync_ship`
 

src/cli-args.ts

@@ -1289,6 +1289,9 @@ function parseSpikeArgs(args: readonly string[]): ParsedCommand {
       json = true;
       continue;
     }
+    if (value?.startsWith('-')) {
+      throw new MethodError(`Unknown option: ${value}\n\n${usage('spike')}`);
+    }
     if (value !== undefined) {
       positionals.push(value);
     }

src/doctor.ts

@@ -806,8 +806,12 @@ function applyRepair(root: string, issue: DoctorIssue): { status: 'applied' | 's
     const updated = raw.replace(/^(cycle:\s*)"[^"]*"\s*$/mu, `$1"${cycleName}"`);
     writeFileSync(flatPath, updated, 'utf8');
 
-    // Remove the old directory (all files should be the single md)
-    rmSync(target, { recursive: true });
+    // Remove the source file, then delete the directory only if empty
+    rmSync(sourceFile);
+    const remaining = readdirSync(target);
+    if (remaining.length === 0) {
+      rmSync(target, { recursive: true });
+    }
 
     // Also rename the corresponding retro directory if it exists
     const configInspection = inspectConfig(root);

src/mcp.ts

@@ -302,16 +302,21 @@ export const MCP_TOOLS: McpToolDef[] = [
   },
   {
     name: 'method_close',
-    description: 'Close an active cycle into its retro packet.',
+    description: 'Close an active cycle into its retro packet. Requires witnessVerified=true to confirm human witness verification.',
     inputSchema: {
       type: 'object',
       properties: {
         ...workspaceProperty,
         cycle: { type: 'string' },
         driftCheck: { type: 'boolean' },
         outcome: { type: 'string', enum: ['hill-met', 'partial', 'not-met'] },
+        witnessVerified: {
+          type: 'boolean',
+          description: 'Human attestation that the witness and human playback questions have been verified.',
+        },
+        summary: { type: 'string', description: 'Retro summary.' },
       },
-      required: ['workspace', 'driftCheck', 'outcome'],
+      required: ['workspace', 'driftCheck', 'outcome', 'witnessVerified'],
     },
   },
   {
@@ -596,7 +601,14 @@ export function createMcpServer(options: CreateMcpServerOptions = {}) {
         const cycleName = validateOptionalString(args.cycle, 'cycle');
         const driftCheck = validateBoolean(args.driftCheck, 'driftCheck');
         const outcome = validateOutcome(args.outcome);
-        const cycle = await workspace.closeCycle(cycleName, driftCheck, outcome);
+        const witnessVerified = validateBoolean(args.witnessVerified, 'witnessVerified');
+        if (!witnessVerified) {
+          throw new Error('witnessVerified must be true — human witness verification is required before closing a cycle.');
+        }
+        const summary = validateOptionalString(args.summary, 'summary');
+        const cycle = await workspace.closeCycle(cycleName, driftCheck, outcome, {
+          summary: summary ?? undefined,
+        });
         return successResult('method_close', `Closed ${cycle.name}`, {
           cycle: relativizeCycle(workspace, cycle),
         });

tests/mcp.test.ts

@@ -839,6 +839,7 @@ describe('MCP Server', () => {
             cycle: 'PROCESS_test-idea-from-mcp',
             driftCheck: true,
             outcome: 'hill-met',
+            witnessVerified: true,
           },
         },
       });