diff --git a/src/cli.ts b/src/cli.ts
index 90306c802a..b9b39a85a8 100644
--- a/src/cli.ts
+++ b/src/cli.ts
@@ -9,13 +9,13 @@ import { registerUtilityCommands } from "./cli/utilityCommands.js";
 import { registerArtifactCommands } from "./cli/artifactCommands.js";
 import { registerManagedCommands } from "./cli/managedCommands.js";
 import { registerEvidenceCommands } from "./cliEvidenceCommands.js";
-import { registerProcessCommands } from "./cliProcessCommands.js";
-import { registerBrowserCommands } from "./cliBrowserCommands.js";
-import { registerAdvancedBrowserCommands } from "./cliBrowserAdvancedCommands.js";
+import { registerProcessCommands } from "./cli/processCommands.js";
+import { registerBrowserCommands } from "./cli/browserCommands.js";
+import { registerAdvancedBrowserCommands } from "./cli/browserAdvancedCommands.js";
 import { registerBrowserScenarioCommands } from "./cliBrowserScenarioCommands.js";
-import { registerElectronCommands } from "./cliElectronCommands.js";
+import { registerElectronCommands } from "./cli/electronCommands.js";
 import { registerJavaScriptRuntimeObservationCommands } from "./cliJavaScriptRuntimeCommands.js";
-import { registerApplicationCommands } from "./cliApplicationCommands.js";
+import { registerApplicationCommands } from "./cli/applicationCommands.js";
 import type { CliInstance } from "./cli/types.js";
 
 /**
diff --git a/src/cliApplicationCommands.ts b/src/cli/applicationCommands.ts
similarity index 79%
rename from src/cliApplicationCommands.ts
rename to src/cli/applicationCommands.ts
index 4172e33ffa..cc11b458d8 100644
--- a/src/cliApplicationCommands.ts
+++ b/src/cli/applicationCommands.ts
@@ -5,30 +5,30 @@ import {
   compareJavaScriptExportShapesEvidenceValidated,
   compareSourceToBundleEvidenceValidated,
   traceApplicationFeatureEvidenceValidated,
-} from "./application/JavaScriptApplicationWorkflowService.js";
-import { traceJavaScriptSemanticsEvidenceValidated } from "./application/JavaScriptSemanticTraceService.js";
+} from "../application/JavaScriptApplicationWorkflowService.js";
+import { traceJavaScriptSemanticsEvidenceValidated } from "../application/JavaScriptSemanticTraceService.js";
 import {
   evaluateReconstructionCoverage,
   reconstructionCoverageEvaluationInputSchema,
-} from "./application/ReconstructionCoverageService.js";
-import { buildReconstructionObligationLedgerEvidenceValidated } from "./application/ReconstructionObligationLedgerService.js";
-import { CLI_COMMANDS } from "./cliCommandNames.js";
-import { parseCliJsonInput } from "./cliJsonInput.js";
-import { logCliCommand } from "./cliLogging.js";
+} from "../application/ReconstructionCoverageService.js";
+import { buildReconstructionObligationLedgerEvidenceValidated } from "../application/ReconstructionObligationLedgerService.js";
+import { CLI_COMMANDS } from "../cliCommandNames.js";
+import { parseCliJsonInput } from "../cliJsonInput.js";
+import { logCliCommand } from "../cliLogging.js";
 import {
   AnalysisInputError,
   projectAnalysisError,
   type AnalysisError,
-} from "./domain/errors.js";
-import { jsonValueSchema, type JsonValue } from "./domain/jsonValue.js";
-import type { Logger } from "./logger.js";
-import { traceApplicationFeatureInputSchema } from "./domain/javascriptFeatureTraceSchemas.js";
-import { traceJavaScriptSemanticsInputSchema } from "./domain/javascriptSemanticTraceSchemas.js";
-import { compareApplicationVersionsInputSchema } from "./domain/javascriptApplicationVersionComparisonSchemas.js";
-import { compareSourceToBundleInputSchema } from "./domain/sourceToBundleComparisonSchemas.js";
-import { compareJavaScriptExportShapesInputSchema } from "./domain/javascriptExportShapeComparisonSchemas.js";
-import { projectInputIssues } from "./domain/inputIssueProjection.js";
-import { reconstructionObligationLedgerInputSchema } from "./domain/reconstructionObligationLedgerSchemas.js";
+} from "../domain/errors.js";
+import { jsonValueSchema, type JsonValue } from "../domain/jsonValue.js";
+import type { Logger } from "../logger.js";
+import { traceApplicationFeatureInputSchema } from "../domain/javascriptFeatureTraceSchemas.js";
+import { traceJavaScriptSemanticsInputSchema } from "../domain/javascriptSemanticTraceSchemas.js";
+import { compareApplicationVersionsInputSchema } from "../domain/javascriptApplicationVersionComparisonSchemas.js";
+import { compareSourceToBundleInputSchema } from "../domain/sourceToBundleComparisonSchemas.js";
+import { compareJavaScriptExportShapesInputSchema } from "../domain/javascriptExportShapeComparisonSchemas.js";
+import { projectInputIssues } from "../domain/inputIssueProjection.js";
+import { reconstructionObligationLedgerInputSchema } from "../domain/reconstructionObligationLedgerSchemas.js";
 
 type CliInstance = ReturnType<typeof Cli.create>;
 
diff --git a/src/cliBrowserAdvancedCommands.ts b/src/cli/browserAdvancedCommands.ts
similarity index 88%
rename from src/cliBrowserAdvancedCommands.ts
rename to src/cli/browserAdvancedCommands.ts
index 1238701198..b699230860 100644
--- a/src/cliBrowserAdvancedCommands.ts
+++ b/src/cli/browserAdvancedCommands.ts
@@ -1,26 +1,26 @@
 import { Cli, z } from "incur";
 
-import { browserContext, browserCliError } from "./cliBrowserContext.js";
-import { browserScopeOptions } from "./cliObservationOptions.js";
+import { browserContext, browserCliError } from "../cliBrowserContext.js";
+import { browserScopeOptions } from "../cliObservationOptions.js";
 import {
   captureWebScreenshot,
   compareWebCaptureEvidence,
   compareWebScreenshotEvidence,
   discoverWebMcpTools,
-} from "./application/BrowserObservationService.js";
-import { CdpBrowserProvider } from "./browser/CdpBrowserProvider.js";
-import { logCliCommand } from "./cliLogging.js";
-import { AnalysisInputError } from "./domain/errors.js";
-import { browserCaptureComparisonInputSchema } from "./domain/browserCaptureComparison.js";
-import { discoverWebMcpToolsInputSchema } from "./domain/webMcpDiscovery.js";
+} from "../application/BrowserObservationService.js";
+import { CdpBrowserProvider } from "../browser/CdpBrowserProvider.js";
+import { logCliCommand } from "../cliLogging.js";
+import { AnalysisInputError } from "../domain/errors.js";
+import { browserCaptureComparisonInputSchema } from "../domain/browserCaptureComparison.js";
+import { discoverWebMcpToolsInputSchema } from "../domain/webMcpDiscovery.js";
 import {
   captureWebScreenshotInputSchema,
   compareWebScreenshotsInputSchema,
-} from "./domain/webScreenshot.js";
-import type { JsonValue } from "./domain/jsonValue.js";
-import { safeParseJson } from "./domain/safeJson.js";
-import type { Logger } from "./logger.js";
-import { CLI_COMMANDS } from "./cliCommandNames.js";
+} from "../domain/webScreenshot.js";
+import type { JsonValue } from "../domain/jsonValue.js";
+import { safeParseJson } from "../domain/safeJson.js";
+import type { Logger } from "../logger.js";
+import { CLI_COMMANDS } from "../cliCommandNames.js";
 
 /** Register WebMCP, capture-diff, and screenshot CLI equivalents. */
 export const registerAdvancedBrowserCommands = (
diff --git a/src/cliBrowserCommands.ts b/src/cli/browserCommands.ts
similarity index 91%
rename from src/cliBrowserCommands.ts
rename to src/cli/browserCommands.ts
index 5587531328..eb7b018279 100644
--- a/src/cliBrowserCommands.ts
+++ b/src/cli/browserCommands.ts
@@ -1,27 +1,27 @@
 import { Cli, z } from "incur";
 
-import { browserContext, browserCliError } from "./cliBrowserContext.js";
+import { browserContext, browserCliError } from "../cliBrowserContext.js";
 import {
   analyzeWebBundle,
   inspectWebPage,
   listBrowserTargets,
   observeWebSession,
-} from "./application/BrowserObservationService.js";
-import { logCliCommand } from "./cliLogging.js";
+} from "../application/BrowserObservationService.js";
+import { logCliCommand } from "../cliLogging.js";
 import {
   inspectWebPageInputSchema,
   listBrowserTargetsInputSchema,
-} from "./domain/browserObservation.js";
-import { analyzeWebBundleInputSchema } from "./domain/webBundleAnalysis.js";
-import { observeWebSessionInputSchema } from "./domain/browserSession.js";
-import { AnalysisInputError } from "./domain/errors.js";
-import type { Logger } from "./logger.js";
-import { CLI_COMMANDS } from "./cliCommandNames.js";
+} from "../domain/browserObservation.js";
+import { analyzeWebBundleInputSchema } from "../domain/webBundleAnalysis.js";
+import { observeWebSessionInputSchema } from "../domain/browserSession.js";
+import { AnalysisInputError } from "../domain/errors.js";
+import type { Logger } from "../logger.js";
+import { CLI_COMMANDS } from "../cliCommandNames.js";
 import {
   browserPageInspectionOptions,
   browserScopeOptions,
   observationDuration,
-} from "./cliObservationOptions.js";
+} from "../cliObservationOptions.js";
 
 /** Register CLI equivalents of the passive browser MCP tools. */
 export const registerBrowserCommands = (
diff --git a/src/cliElectronCommands.ts b/src/cli/electronCommands.ts
similarity index 85%
rename from src/cliElectronCommands.ts
rename to src/cli/electronCommands.ts
index c5e8ad5700..277246750f 100644
--- a/src/cliElectronCommands.ts
+++ b/src/cli/electronCommands.ts
@@ -3,27 +3,27 @@ import { Cli, z } from "incur";
 import {
   inspectElectronPage,
   listElectronTargets,
-} from "./application/ElectronObservationService.js";
-import { captureElectronScenario } from "./application/ElectronActiveObservationService.js";
-import { reconcileJavaScriptRuntimeEvidence } from "./application/JavaScriptRuntimeReconciliationService.js";
-import { CdpElectronProvider } from "./browser/CdpElectronProvider.js";
-import { PlaywrightElectronActiveProvider } from "./browser/PlaywrightElectronActiveProvider.js";
-import { logCliCommand } from "./cliLogging.js";
+} from "../application/ElectronObservationService.js";
+import { captureElectronScenario } from "../application/ElectronActiveObservationService.js";
+import { reconcileJavaScriptRuntimeEvidence } from "../application/JavaScriptRuntimeReconciliationService.js";
+import { CdpElectronProvider } from "../browser/CdpElectronProvider.js";
+import { PlaywrightElectronActiveProvider } from "../browser/PlaywrightElectronActiveProvider.js";
+import { logCliCommand } from "../cliLogging.js";
 import {
   inspectElectronPageInputSchema,
   listElectronTargetsInputSchema,
-} from "./domain/electronObservation.js";
-import { electronActiveObservationInputSchema } from "./domain/electronActiveObservation.js";
-import { AnalysisInputError, projectAnalysisError } from "./domain/errors.js";
-import type { JsonValue } from "./domain/jsonValue.js";
-import type { Logger } from "./logger.js";
-import { CLI_COMMANDS } from "./cliCommandNames.js";
-import { parseCliJsonInput } from "./cliJsonInput.js";
+} from "../domain/electronObservation.js";
+import { electronActiveObservationInputSchema } from "../domain/electronActiveObservation.js";
+import { AnalysisInputError, projectAnalysisError } from "../domain/errors.js";
+import type { JsonValue } from "../domain/jsonValue.js";
+import type { Logger } from "../logger.js";
+import { CLI_COMMANDS } from "../cliCommandNames.js";
+import { parseCliJsonInput } from "../cliJsonInput.js";
 import {
   electronPageInspectionOptions,
   javascriptApplicationOptions,
-} from "./cliObservationOptions.js";
-import { runCliJavaScriptApplicationAnalysis } from "./cli/javascriptApplicationAnalysis.js";
+} from "../cliObservationOptions.js";
+import { runCliJavaScriptApplicationAnalysis } from "./javascriptApplicationAnalysis.js";
 
 /** Register CLI equivalents of the Electron MCP tools. */
 export const registerElectronCommands = (
diff --git a/src/cliSetup.ts b/src/cli/interactiveSetup.ts
similarity index 98%
rename from src/cliSetup.ts
rename to src/cli/interactiveSetup.ts
index e378985f6b..f1d2db70a8 100644
--- a/src/cliSetup.ts
+++ b/src/cli/interactiveSetup.ts
@@ -14,8 +14,8 @@ import type {
   SetupClientState,
   SetupProgressEvent,
   SetupResult,
-} from "./application/SetupTypes.js";
-import { SUPPORTED_CLIENT_DEFINITIONS } from "./application/SupportedClients.js";
+} from "../application/SetupTypes.js";
+import { SUPPORTED_CLIENT_DEFINITIONS } from "../application/SupportedClients.js";
 
 const clientDisplayNames: ReadonlyMap<string, string> = new Map(
   SUPPORTED_CLIENT_DEFINITIONS.map(({ name, displayName }) => [
diff --git a/src/cliProcessCommands.ts b/src/cli/processCommands.ts
similarity index 88%
rename from src/cliProcessCommands.ts
rename to src/cli/processCommands.ts
index 9b8b8827d6..e68059b7c4 100644
--- a/src/cliProcessCommands.ts
+++ b/src/cli/processCommands.ts
@@ -4,10 +4,10 @@ import {
   captureProcessScenarioFile,
   compareProcessEvidenceFiles,
   isProcessCliFailure,
-} from "./application/ProcessCli.js";
-import { logCliCommand } from "./cliLogging.js";
-import type { Logger } from "./logger.js";
-import { CLI_COMMANDS } from "./cliCommandNames.js";
+} from "../application/ProcessCli.js";
+import { logCliCommand } from "../cliLogging.js";
+import type { Logger } from "../logger.js";
+import { CLI_COMMANDS } from "../cliCommandNames.js";
 
 /** Register direct process capture and comparison commands. */
 export const registerProcessCommands = (
diff --git a/src/cli/setupCommands.ts b/src/cli/setupCommands.ts
index 6648aa26a1..2bcec6ff36 100644
--- a/src/cli/setupCommands.ts
+++ b/src/cli/setupCommands.ts
@@ -5,12 +5,12 @@ import {
   runDoctor,
   type DoctorScope,
 } from "../application/Doctor.js";
-import { runSetup } from "../application/Setup.js";
-import { systemSetupHost } from "../application/SetupHost.js";
 import {
   isSetupFailure,
   type SetupOptions,
 } from "../application/SetupTypes.js";
+import { runSetup } from "../application/Setup.js";
+import { systemSetupHost } from "../application/SetupHost.js";
 import { isUninstallFailure, runUninstall } from "../application/Uninstall.js";
 import { isUpdateFailure, runUpdate } from "../application/Update.js";
 import { systemUpdateHost } from "../application/UpdateRuntime.js";
@@ -18,7 +18,7 @@ import {
   confirmInteractiveSetup,
   renderInteractiveSetupResult,
   renderSetupProgress,
-} from "../cliSetup.js";
+} from "./interactiveSetup.js";
 import { PRODUCT_IDENTITY } from "../identity.js";
 import { logCliCommand } from "../cliLogging.js";
 import { createSystemDoctorHost } from "../doctorRuntime.js";
diff --git a/tests/boundary/cli/cliSetup.test.ts b/tests/boundary/cli/cliSetup.test.ts
index a4740f4be0..c10aa66d8a 100644
--- a/tests/boundary/cli/cliSetup.test.ts
+++ b/tests/boundary/cli/cliSetup.test.ts
@@ -227,7 +227,7 @@ describe("interactive setup completion", () => {
           "--input-type=module",
           "--eval",
           [
-            'import { renderInteractiveSetupResult } from "./dist/cliSetup.js";',
+            'import { renderInteractiveSetupResult } from "./dist/cli/interactiveSetup.js";',
             "renderInteractiveSetupResult({",
             '  status: "ready",',
             "  plannedActions: [],",
@@ -287,7 +287,7 @@ const runJourney = async (
 ): Promise<JourneyResult> => {
   const isolatedHome = await createTestTempDirectory("rea-cli-setup-test-");
   const script = [
-    'import { confirmInteractiveSetup } from "./dist/cliSetup.js";',
+    'import { confirmInteractiveSetup } from "./dist/cli/interactiveSetup.js";',
     `const actions = ${JSON.stringify(journeyActions)};`,
     `const context = ${JSON.stringify({ stage: "select", clientStates, selectedClientIds: initialClientIds, clientSelectionAllowed: true })};`,
     `let decision = await confirmInteractiveSetup(actions, ${JSON.stringify(accessible)}, context);`,