diff --git a/.changeset/skip-hand-written-contracts.md b/.changeset/skip-hand-written-contracts.md
new file mode 100644
index 000000000..2802f9eba
--- /dev/null
+++ b/.changeset/skip-hand-written-contracts.md
@@ -0,0 +1,5 @@
+---
+"@qawolf/cli": patch
+---
+
+Skip public-API command generation for contracts served by hand-written commands, so a future `flow.list` contract does not mint a duplicate of `qawolf flows list --remote`.
diff --git a/.claude/rules/domain-structure.md b/.claude/rules/domain-structure.md
index d8a206de9..38a5eebb1 100644
--- a/.claude/rules/domain-structure.md
+++ b/.claude/rules/domain-structure.md
@@ -14,7 +14,7 @@ Import rules are enforced by oxlint:
 
 ## Adding a command
 
-There are two registration patterns. Commands that expose a platform public-API endpoint are generated from contracts by `registerPublicApiCommands` (`src/commands/publicApi/`) — adding the contract to `@qawolf/api-contracts` and updating the dependency is all it takes. Commands with local logic or multi-step UX flows are hand-written under `src/commands/<domain>/` following the steps below. Never register the same endpoint both ways — the generated path throws on command collisions.
+There are two registration patterns. Commands that expose a platform public-API endpoint are generated from contracts by `registerPublicApiCommands` (`src/commands/publicApi/`) — adding the contract to `@qawolf/api-contracts` and updating the dependency is all it takes. Commands with local logic or multi-step UX flows are hand-written under `src/commands/<domain>/` following the steps below. Never register the same endpoint both ways — the generated path throws on command collisions. When a contract's endpoint is served by a hand-written command, add its name to `handWrittenContractNames` in `src/commands/publicApi/index.ts` so the generator skips it.
 
 1. Create the handler directory under `src/commands/<domain>/`
 2. Export a registration function (`registerXCommand`) that takes a Commander `program` instance
diff --git a/AGENTS.md b/AGENTS.md
index 8282ed979..82a616a22 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -81,7 +81,7 @@ The codebase is organized into four strict layers. **`core/`** holds pure functi
 
 API clients (tRPC for the QA Wolf platform, GitHub REST) live in `src/shell/platform/` and `src/shell/` respectively — one module per auth boundary.
 
-Commands register in one of two ways: platform public-API endpoints are generated from contracts via `registerPublicApiCommands` (`src/commands/publicApi/`), while commands with local logic or multi-step UX flows are hand-written under `src/commands/<domain>/`. Never both for the same endpoint. See `.claude/rules/domain-structure.md` ("Adding a command") for the full decision rule.
+Commands register in one of two ways: platform public-API endpoints are generated from contracts via `registerPublicApiCommands` (`src/commands/publicApi/`), while commands with local logic or multi-step UX flows are hand-written under `src/commands/<domain>/`. Never both for the same endpoint — contracts served by a hand-written command go in the generator's skip-list (`handWrittenContractNames`). See `.claude/rules/domain-structure.md` ("Adding a command") for the full decision rule.
 
 ## Code Style
 
diff --git a/src/commands/publicApi/index.test.ts b/src/commands/publicApi/index.test.ts
index 9e162dd60..2a22c9215 100644
--- a/src/commands/publicApi/index.test.ts
+++ b/src/commands/publicApi/index.test.ts
@@ -134,6 +134,37 @@ describe("registerPublicApiCommands", () => {
     ).toThrow('Generated command "run create" collides');
   });
 
+  it("skips contracts served by hand-written commands", () => {
+    const listContract = {
+      description: "List the flows of an environment.",
+      input: z.object({ environmentId: z.string() }),
+      kind: "read",
+      name: "flow.list",
+      output: z.object({ flows: z.array(z.object({ flowId: z.string() })) }),
+    } as const;
+    const getContract = {
+      description: "Look up a run.",
+      input: z.object({ runId: z.string() }),
+      kind: "read",
+      name: "run.get",
+      output: z.object({ status: z.string() }),
+    } as const;
+    const program = makeProgram();
+
+    registerPublicApiCommands(program, createSignalRegistry(), {
+      contracts: { flow: { list: listContract }, run: { get: getContract } },
+    });
+
+    // No `flow` group either: skipped contracts create no empty namespaces.
+    expect(
+      program.commands.find((command) => command.name() === "flow"),
+    ).toBeUndefined();
+    const run = program.commands.find((command) => command.name() === "run");
+    expect(
+      run?.commands.find((command) => command.name() === "get"),
+    ).toBeDefined();
+  });
+
   it("registers nested namespaces from custom contract trees", () => {
     const contract = {
       description: "Look up a run attempt.",
diff --git a/src/commands/publicApi/index.ts b/src/commands/publicApi/index.ts
index cc6fc790c..7573378ee 100644
--- a/src/commands/publicApi/index.ts
+++ b/src/commands/publicApi/index.ts
@@ -26,6 +26,10 @@ const groupDescriptions: Record<string, string> = {
   run: "Trigger and manage QA Wolf runs on the platform",
 };
 
+// Contracts already served by hand-written commands; the generator must not
+// mint duplicates (flow.list is served by `qawolf flows list --remote`).
+const handWrittenContractNames: ReadonlySet<string> = new Set(["flow.list"]);
+
 function resolveGroup(parent: Command, segment: string): Command {
   const existing = parent.commands.find(
     (command) => command.name() === segment,
@@ -90,7 +94,9 @@ export function registerPublicApiCommands(
   signals: SignalRegistry,
   options: Options = {},
 ): void {
-  const specs = buildCommandSpecs(options.contracts ?? publicContractsV1);
+  const specs = buildCommandSpecs(options.contracts ?? publicContractsV1, {
+    skipContractNames: handWrittenContractNames,
+  });
   for (const spec of specs) {
     registerSpec(program, signals, spec, options.authDeps);
   }
diff --git a/src/domains/publicApi/commandSpecs.test.ts b/src/domains/publicApi/commandSpecs.test.ts
index 4e8422b66..668445d8a 100644
--- a/src/domains/publicApi/commandSpecs.test.ts
+++ b/src/domains/publicApi/commandSpecs.test.ts
@@ -26,6 +26,32 @@ describe("buildCommandSpecs", () => {
     ]);
   });
 
+  it("skips contracts named in skipContractNames without building their specs", () => {
+    // Unmappable input proves the skip happens before flag building: a
+    // hand-written contract never has to be expressible as generated flags.
+    const skipped = {
+      description: "Hand-written elsewhere",
+      input: z.object({ config: z.object({ nested: z.string() }) }),
+      kind: "read",
+      name: "flow.list",
+      output: z.object({}),
+    } as const;
+    const kept = {
+      description: "Generated",
+      input: z.object({ runId: z.string() }),
+      kind: "read",
+      name: "run.get",
+      output: z.object({}),
+    } as const;
+
+    const specs = buildCommandSpecs(
+      { flow: { list: skipped }, run: { get: kept } },
+      { skipContractNames: new Set(["flow.list"]) },
+    );
+
+    expect(specs.map((spec) => spec.trpcPath)).toEqual(["public.run.get"]);
+  });
+
   it("throws when a contract name does not match its position in the tree", () => {
     const contract = {
       description: "Mismatched",
diff --git a/src/domains/publicApi/commandSpecs.ts b/src/domains/publicApi/commandSpecs.ts
index e43e5a10b..52b6e08cb 100644
--- a/src/domains/publicApi/commandSpecs.ts
+++ b/src/domains/publicApi/commandSpecs.ts
@@ -56,12 +56,23 @@ function buildSpec(
   };
 }
 
-export function buildCommandSpecs(tree: ContractTree): CommandSpec[] {
+type BuildOptions = {
+  // Contracts served by hand-written commands. Skipped before spec building,
+  // so a hand-written contract never has to be expressible as generated flags.
+  skipContractNames?: ReadonlySet<string>;
+};
+
+export function buildCommandSpecs(
+  tree: ContractTree,
+  options: BuildOptions = {},
+): CommandSpec[] {
+  const skip = options.skipContractNames;
   const walk = (node: ContractTree, path: string[]): CommandSpec[] =>
-    Object.entries(node).flatMap(([key, value]) =>
-      isContract(value)
-        ? [buildSpec(value, [...path, key])]
-        : walk(value, [...path, key]),
-    );
+    Object.entries(node).flatMap(([key, value]) => {
+      const childPath = [...path, key];
+      if (!isContract(value)) return walk(value, childPath);
+      if (skip?.has(childPath.join("."))) return [];
+      return [buildSpec(value, childPath)];
+    });
   return walk(tree, []);
 }