diff --git a/CONTEXT.md b/CONTEXT.md
index cb9a1a527..203982abb 100644
--- a/CONTEXT.md
+++ b/CONTEXT.md
@@ -59,7 +59,7 @@ Canonical command normalization and resolution Interface (`query-command-resolut
 Module owning command resolution, policy projection (`mutation`, `output_mode`), unknown-command diagnosis, and handler Adapter binding at one seam for query dispatch.
 
 ### Init Command Module
-SDK Module owning the `init.*` family of query handlers that compose atomic SDK queries into the flat JSON bundles consumed by init workflows (`/gsd-execute-phase`, `/gsd-plan-phase`, `/gsd-verify-work`, `/gsd-new-project`, `/gsd-manager`, `/gsd-progress`, `/gsd-resume`, etc.). Divided into two source files: `sdk/src/query/init.ts` (13 basic handlers plus `withProjectRoot` project-identity injection) and `sdk/src/query/init-complex.ts` (the 3 heavyweight handlers: `initNewProject`, `initProgress`, `initManager`). All handlers return `{ data: <flat JSON> }` aligned with the CJS `bin/lib/init.cjs` surface. Test seams: `sdk/src/query/init.test.ts` (basic handlers + withProjectRoot precedence), `sdk/src/query/init-complex.test.ts` (complex handlers + progress/manager precedence regression #2674 + workstream scoping regression #3196), `sdk/src/query/init-workstream-milestone-op.test.ts` (initMilestoneOp + roadmapAnalyze + resolveQueryRuntimeContext workstream fallback). CJS CLI surface tested in `tests/init.test.cjs` and `tests/init-manager.test.cjs` (includes cross-milestone dependency regression #2267).
+SDK Module owning the `init.*` family of query handlers that compose atomic SDK queries into the flat JSON bundles consumed by init workflows (`/gsd-execute-phase`, `/gsd-plan-phase`, `/gsd-verify-work`, `/gsd-new-project`, `/gsd-manager`, `/gsd-progress`, `/gsd-resume`, etc.). Divided into two source files: `sdk/src/handlers/init/composer.ts` (13 basic handlers plus `withProjectRoot` project-identity injection) and `sdk/src/handlers/init/complex.ts` (the 3 heavyweight handlers: `initNewProject`, `initProgress`, `initManager`). All handlers return `{ data: <flat JSON> }` aligned with the CJS `bin/lib/init.cjs` surface. Test seams: `sdk/src/query/init.test.ts` (basic handlers + withProjectRoot precedence), `sdk/src/query/init-complex.test.ts` (complex handlers + progress/manager precedence regression #2674 + workstream scoping regression #3196), `sdk/src/query/init-workstream-milestone-op.test.ts` (initMilestoneOp + roadmapAnalyze + resolveQueryRuntimeContext workstream fallback). CJS CLI surface tested in `tests/init.test.cjs` and `tests/init-manager.test.cjs` (includes cross-milestone dependency regression #2267).
 
 ### CJS Command Router Adapter Module
 Compatibility Adapter Module for `gsd-tools.cjs` command families. Uses generated command metadata plus small argument shapers to route to CJS handlers, rather than calling SDK Command Topology directly. Preserves CJS compatibility startup while reducing hand-written router drift. Per-family migration to call the **Sync Runtime Bridge Module**'s `executeForCjs` in-process — eliminating the remaining parallel CJS handler implementations — is the active work of #3524 Phase 5; the primitive itself ships in #3555, with each canonical command family (`state.*`, `verify.*`, `init.*`, `phase.*`, `phases.*`, `validate.*`, `roadmap.*`, `frontmatter.*`, `config.*`) routing through `executeForCjs` in its own follow-up enhancement.
diff --git a/sdk/src/query/init-complex.ts b/sdk/src/handlers/init/complex.ts
similarity index 98%
rename from sdk/src/query/init-complex.ts
rename to sdk/src/handlers/init/complex.ts
index 5e13c738d..2fb1bcff9 100644
--- a/sdk/src/query/init-complex.ts
+++ b/sdk/src/handlers/init/complex.ts
@@ -11,7 +11,7 @@
  *
  * @example
  * ```typescript
- * import { initProgress, initManager } from './init-complex.js';
+ * import { initProgress, initManager } from './complex.js';
  *
  * const result = await initProgress([], '/project');
  * // { data: { phases: [...], milestone_version: 'v3.0', ... } }
@@ -24,8 +24,8 @@ import { readFile } from 'node:fs/promises';
 import { join, relative } from 'node:path';
 import { homedir } from 'node:os';
 
-import { loadConfig } from '../config.js';
-import { resolveModel } from './config-query.js';
+import { loadConfig } from '../../config.js';
+import { resolveModel } from '../../query/config-query.js';
 import {
   detectRuntime,
   planningPaths,
@@ -33,16 +33,16 @@ import {
   phaseTokenMatches,
   resolveAgentsDir,
   toPosixPath,
-} from './helpers.js';
+} from '../../query/helpers.js';
 import {
   getMilestoneInfo,
   extractCurrentMilestone,
   extractNextMilestoneSection,
   extractPhasesFromSection,
-} from './roadmap.js';
-import { agentSkills } from './skills.js';
-import { withProjectRoot } from './init.js';
-import type { QueryHandler } from './utils.js';
+} from '../../query/roadmap.js';
+import { agentSkills } from '../../query/skills.js';
+import { withProjectRoot } from './composer.js';
+import type { QueryHandler } from '../../query/utils.js';
 
 // ─── Internal helpers ──────────────────────────────────────────────────────
 
diff --git a/sdk/src/query/init.ts b/sdk/src/handlers/init/composer.ts
similarity index 98%
rename from sdk/src/query/init.ts
rename to sdk/src/handlers/init/composer.ts
index a310c63cd..b0a857574 100644
--- a/sdk/src/query/init.ts
+++ b/sdk/src/handlers/init/composer.ts
@@ -6,11 +6,11 @@
  * follows the QueryHandler signature and returns { data: <flat JSON> }.
  *
  * Port of get-shit-done/bin/lib/init.cjs (13 of 16 handlers).
- * The 3 complex handlers (new-project, progress, manager) are in init-complex.ts.
+ * The 3 complex handlers (new-project, progress, manager) are in complex.ts.
  *
  * @example
  * ```typescript
- * import { initExecutePhase, withProjectRoot } from './init.js';
+ * import { initExecutePhase, withProjectRoot } from './composer.js';
  *
  * const result = await initExecutePhase(['9'], '/project');
  * // { data: { executor_model: 'opus', phase_found: true, ... } }
@@ -22,18 +22,18 @@ import { readFile, readdir } from 'node:fs/promises';
 import { join, relative, basename } from 'node:path';
 import { execSync } from 'node:child_process';
 import { homedir } from 'node:os';
-import { GSDError, ErrorClassification } from '../errors.js';
+import { GSDError, ErrorClassification } from '../../errors.js';
 
-import { loadConfig, type GSDConfig } from '../config.js';
-import { resolveModel, MODEL_PROFILES } from './config-query.js';
-import { maskIfSecret } from './secrets.js';
-import { findPhase } from './phase.js';
-import { getMilestonePhaseFilter } from './state.js';
-import { roadmapGetPhase, getMilestoneInfo, extractCurrentMilestone, extractPhasesFromSection } from './roadmap.js';
-import { determinePhaseStatus } from './progress.js';
-import { planningPaths, normalizePhaseName, toPosixPath, resolveAgentsDir, detectRuntime } from './helpers.js';
-import { generatePhaseSlug, assertSafeProjectCode } from './phase-lifecycle-policy.js';
-import type { QueryHandler } from './utils.js';
+import { loadConfig, type GSDConfig } from '../../config.js';
+import { resolveModel, MODEL_PROFILES } from '../../query/config-query.js';
+import { maskIfSecret } from '../../query/secrets.js';
+import { findPhase } from '../../query/phase.js';
+import { getMilestonePhaseFilter } from '../../query/state.js';
+import { roadmapGetPhase, getMilestoneInfo, extractCurrentMilestone, extractPhasesFromSection } from '../../query/roadmap.js';
+import { determinePhaseStatus } from '../../query/progress.js';
+import { planningPaths, normalizePhaseName, toPosixPath, resolveAgentsDir, detectRuntime } from '../../query/helpers.js';
+import { generatePhaseSlug, assertSafeProjectCode } from '../../query/phase-lifecycle-policy.js';
+import type { QueryHandler } from '../../query/utils.js';
 
 // ─── Internal helpers ──────────────────────────────────────────────────────
 
diff --git a/sdk/src/query/command-family-handlers.ts b/sdk/src/query/command-family-handlers.ts
index d3b00f103..f90a2802e 100644
--- a/sdk/src/query/command-family-handlers.ts
+++ b/sdk/src/query/command-family-handlers.ts
@@ -34,8 +34,8 @@ import {
   initIngestDocs, initResume, initVerifyWork, initPhaseOp, initTodos,
   initMilestoneOp, initMapCodebase, initNewWorkspace,
   initListWorkspaces, initRemoveWorkspace,
-} from './init.js';
-import { initNewProject, initProgress, initManager } from './init-complex.js';
+} from '../handlers/init/composer.js';
+import { initNewProject, initProgress, initManager } from '../handlers/init/complex.js';
 
 export const FAMILY_HANDLERS: Record<string, Readonly<Record<string, QueryHandler>>> = {
   state: {
diff --git a/sdk/src/query/init-complex.test.ts b/sdk/src/query/init-complex.test.ts
index d780fb343..d1bf450b3 100644
--- a/sdk/src/query/init-complex.test.ts
+++ b/sdk/src/query/init-complex.test.ts
@@ -9,7 +9,7 @@ import { describe, it, expect, beforeEach, afterEach } from 'vitest';
 import { mkdtemp, writeFile, mkdir, rm } from 'node:fs/promises';
 import { join } from 'node:path';
 import { tmpdir } from 'node:os';
-import { initNewProject, initProgress, initManager } from './init-complex.js';
+import { initNewProject, initProgress, initManager } from '../handlers/init/complex.js';
 
 let tmpDir: string;
 let previousGsdAgentsDir: string | undefined;
diff --git a/sdk/src/query/init-workstream-milestone-op.test.ts b/sdk/src/query/init-workstream-milestone-op.test.ts
index 6edc3a929..c39f2bf33 100644
--- a/sdk/src/query/init-workstream-milestone-op.test.ts
+++ b/sdk/src/query/init-workstream-milestone-op.test.ts
@@ -11,7 +11,7 @@ import { mkdtemp, mkdir, rm, writeFile } from 'node:fs/promises';
 import { join } from 'node:path';
 import { tmpdir } from 'node:os';
 
-import { initMilestoneOp } from './init.js';
+import { initMilestoneOp } from '../handlers/init/composer.js';
 import { roadmapAnalyze } from './roadmap.js';
 import { resolveQueryRuntimeContext } from './query-runtime-context.js';
 
diff --git a/sdk/src/query/init.test.ts b/sdk/src/query/init.test.ts
index 2fd1c66c0..9bc9d492d 100644
--- a/sdk/src/query/init.test.ts
+++ b/sdk/src/query/init.test.ts
@@ -25,7 +25,7 @@ import {
   initListWorkspaces,
   initRemoveWorkspace,
   initIngestDocs,
-} from './init.js';
+} from '../handlers/init/composer.js';
 
 let tmpDir: string;
 
diff --git a/sdk/src/runtime/name-policy.ts b/sdk/src/runtime/name-policy.ts
index a4cf85940..7ab84ab51 100644
--- a/sdk/src/runtime/name-policy.ts
+++ b/sdk/src/runtime/name-policy.ts
@@ -1,6 +1,6 @@
 import { readFileSync } from 'node:fs';
 import { fileURLToPath } from 'node:url';
-import { SUPPORTED_RUNTIMES, type Runtime } from './model-catalog.js';
+import { SUPPORTED_RUNTIMES, type Runtime } from '../model-catalog.js';
 
 interface RuntimeAliasManifest {
   [canonicalRuntime: string]: string[];
@@ -29,4 +29,3 @@ export function canonicalizeRuntimeName(value: unknown): Runtime | null {
   if (typeof value !== 'string') return null;
   return aliasToCanonical.get(normalizeRuntimeToken(value)) ?? null;
 }
-