diff --git a/packages/cli/package.json b/packages/cli/package.json
index 29d947a311..94e60c03af 100644
--- a/packages/cli/package.json
+++ b/packages/cli/package.json
@@ -81,7 +81,7 @@
     "buffer": "^6.0.3",
     "chalk": "^4.0.0",
     "chokidar": "^3.3.1",
-    "cleye": "^2.2.1",
+    "cleye": "^2.3.0",
     "commander": "^14.0.3",
     "cross-fetch": "^4.0.0",
     "cross-spawn": "^7.0.3",
diff --git a/packages/cli/src/modules/build/commands/buildWorkspace.ts b/packages/cli/src/modules/build/commands/buildWorkspace.ts
index 649171d7d8..f9ca19962f 100644
--- a/packages/cli/src/modules/build/commands/buildWorkspace.ts
+++ b/packages/cli/src/modules/build/commands/buildWorkspace.ts
@@ -38,6 +38,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: { ...info, usage: `${info.usage} <workspace-dir> [packages...]` },
+      booleanFlagNegation: true,
       parameters: ['<workspace-dir>', '[packages...]'],
       flags: {
         alwaysPack: {
diff --git a/packages/cli/src/modules/build/commands/package/build/command.ts b/packages/cli/src/modules/build/commands/package/build/command.ts
index 8c802fe2b5..7a6280299b 100644
--- a/packages/cli/src/modules/build/commands/package/build/command.ts
+++ b/packages/cli/src/modules/build/commands/package/build/command.ts
@@ -44,6 +44,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         role: {
           type: String,
diff --git a/packages/cli/src/modules/build/commands/package/clean.ts b/packages/cli/src/modules/build/commands/package/clean.ts
index f222c23666..6aa987f6c1 100644
--- a/packages/cli/src/modules/build/commands/package/clean.ts
+++ b/packages/cli/src/modules/build/commands/package/clean.ts
@@ -20,7 +20,7 @@ import { targetPaths } from '@backstage/cli-common';
 import type { CommandContext } from '../../../../wiring/types';
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
   await fs.remove(targetPaths.resolve('dist'));
   await fs.remove(targetPaths.resolve('dist-types'));
   await fs.remove(targetPaths.resolve('coverage'));
diff --git a/packages/cli/src/modules/build/commands/package/postpack.ts b/packages/cli/src/modules/build/commands/package/postpack.ts
index 8ca1c800ce..232d03af6b 100644
--- a/packages/cli/src/modules/build/commands/package/postpack.ts
+++ b/packages/cli/src/modules/build/commands/package/postpack.ts
@@ -20,6 +20,6 @@ import { revertProductionPack } from '../../lib/packager/productionPack';
 import type { CommandContext } from '../../../../wiring/types';
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
   await revertProductionPack(targetPaths.dir);
 };
diff --git a/packages/cli/src/modules/build/commands/package/prepack.ts b/packages/cli/src/modules/build/commands/package/prepack.ts
index 39d92518bc..e6aba2ce3f 100644
--- a/packages/cli/src/modules/build/commands/package/prepack.ts
+++ b/packages/cli/src/modules/build/commands/package/prepack.ts
@@ -23,7 +23,7 @@ import { createTypeDistProject } from '../../lib/typeDistProject';
 import type { CommandContext } from '../../../../wiring/types';
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
 
   publishPreflightCheck({
     dir: targetPaths.dir,
diff --git a/packages/cli/src/modules/build/commands/package/start/command.ts b/packages/cli/src/modules/build/commands/package/start/command.ts
index 143385e4a6..fe871973de 100644
--- a/packages/cli/src/modules/build/commands/package/start/command.ts
+++ b/packages/cli/src/modules/build/commands/package/start/command.ts
@@ -36,6 +36,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         config: {
           type: [String],
diff --git a/packages/cli/src/modules/build/commands/repo/build.ts b/packages/cli/src/modules/build/commands/repo/build.ts
index b1e0239b4b..7140310464 100644
--- a/packages/cli/src/modules/build/commands/repo/build.ts
+++ b/packages/cli/src/modules/build/commands/repo/build.ts
@@ -37,6 +37,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         all: {
           type: Boolean,
diff --git a/packages/cli/src/modules/build/commands/repo/clean.ts b/packages/cli/src/modules/build/commands/repo/clean.ts
index efafdae510..7814c1e4b7 100644
--- a/packages/cli/src/modules/build/commands/repo/clean.ts
+++ b/packages/cli/src/modules/build/commands/repo/clean.ts
@@ -22,7 +22,7 @@ import { run, targetPaths } from '@backstage/cli-common';
 import type { CommandContext } from '../../../../wiring/types';
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
   const packages = await PackageGraph.listTargetPackages();
 
   await fs.remove(targetPaths.resolveRoot('dist'));
diff --git a/packages/cli/src/modules/build/commands/repo/start.ts b/packages/cli/src/modules/build/commands/repo/start.ts
index 6acd4f1463..e4c51a1e46 100644
--- a/packages/cli/src/modules/build/commands/repo/start.ts
+++ b/packages/cli/src/modules/build/commands/repo/start.ts
@@ -42,6 +42,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: { ...info, usage: `${info.usage} [packages...]` },
+      booleanFlagNegation: true,
       parameters: ['[packages...]'],
       flags: {
         plugin: {
diff --git a/packages/cli/src/modules/config/commands/docs.ts b/packages/cli/src/modules/config/commands/docs.ts
index ed949c695f..84d2f384e1 100644
--- a/packages/cli/src/modules/config/commands/docs.ts
+++ b/packages/cli/src/modules/config/commands/docs.ts
@@ -31,6 +31,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         package: {
           type: String,
diff --git a/packages/cli/src/modules/config/commands/print.ts b/packages/cli/src/modules/config/commands/print.ts
index 412fdd69ff..33f7245604 100644
--- a/packages/cli/src/modules/config/commands/print.ts
+++ b/packages/cli/src/modules/config/commands/print.ts
@@ -27,6 +27,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         package: { type: String, description: 'Package to print config for' },
         lax: {
diff --git a/packages/cli/src/modules/config/commands/schema.ts b/packages/cli/src/modules/config/commands/schema.ts
index b41264e4b7..13f651534c 100644
--- a/packages/cli/src/modules/config/commands/schema.ts
+++ b/packages/cli/src/modules/config/commands/schema.ts
@@ -28,6 +28,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         package: { type: String, description: 'Package to print schema for' },
         format: { type: String, description: 'Output format (yaml or json)' },
diff --git a/packages/cli/src/modules/config/commands/validate.ts b/packages/cli/src/modules/config/commands/validate.ts
index abbbd7a176..f6cf9cc662 100644
--- a/packages/cli/src/modules/config/commands/validate.ts
+++ b/packages/cli/src/modules/config/commands/validate.ts
@@ -24,6 +24,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         package: {
           type: String,
diff --git a/packages/cli/src/modules/create-github-app/commands/create-github-app/index.ts b/packages/cli/src/modules/create-github-app/commands/create-github-app/index.ts
index 1cd51e541b..9dd9f4c4c4 100644
--- a/packages/cli/src/modules/create-github-app/commands/create-github-app/index.ts
+++ b/packages/cli/src/modules/create-github-app/commands/create-github-app/index.ts
@@ -32,6 +32,7 @@ export default async ({ args, info }: CommandContext) => {
   const { _: positionals } = cli(
     {
       help: { ...info, usage: `${info.usage} <github-org>` },
+      booleanFlagNegation: true,
       parameters: ['<github-org>'],
     },
     undefined,
diff --git a/packages/cli/src/modules/info/commands/info.ts b/packages/cli/src/modules/info/commands/info.ts
index c423d2b1dc..ab26714fca 100644
--- a/packages/cli/src/modules/info/commands/info.ts
+++ b/packages/cli/src/modules/info/commands/info.ts
@@ -58,6 +58,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         include: {
           type: [String],
diff --git a/packages/cli/src/modules/lint/commands/package/lint.ts b/packages/cli/src/modules/lint/commands/package/lint.ts
index 40062726f1..39c74bab73 100644
--- a/packages/cli/src/modules/lint/commands/package/lint.ts
+++ b/packages/cli/src/modules/lint/commands/package/lint.ts
@@ -27,6 +27,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: { ...info, usage: `${info.usage} [directories...]` },
+      booleanFlagNegation: true,
       parameters: ['[directories...]'],
       flags: {
         fix: {
diff --git a/packages/cli/src/modules/lint/commands/repo/lint.ts b/packages/cli/src/modules/lint/commands/repo/lint.ts
index 174282ffcf..5ce4be72f8 100644
--- a/packages/cli/src/modules/lint/commands/repo/lint.ts
+++ b/packages/cli/src/modules/lint/commands/repo/lint.ts
@@ -66,6 +66,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         fix: {
           type: Boolean,
diff --git a/packages/cli/src/modules/maintenance/commands/repo/fix.ts b/packages/cli/src/modules/maintenance/commands/repo/fix.ts
index ea367d813a..dc2e554121 100644
--- a/packages/cli/src/modules/maintenance/commands/repo/fix.ts
+++ b/packages/cli/src/modules/maintenance/commands/repo/fix.ts
@@ -501,6 +501,7 @@ export default async ({
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         publish: {
           type: Boolean,
diff --git a/packages/cli/src/modules/maintenance/commands/repo/list-deprecations.ts b/packages/cli/src/modules/maintenance/commands/repo/list-deprecations.ts
index 3b081119ee..23f64463cb 100644
--- a/packages/cli/src/modules/maintenance/commands/repo/list-deprecations.ts
+++ b/packages/cli/src/modules/maintenance/commands/repo/list-deprecations.ts
@@ -28,6 +28,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         json: { type: Boolean, description: 'Output as JSON' },
       },
diff --git a/packages/cli/src/modules/migrate/commands/packageExports.ts b/packages/cli/src/modules/migrate/commands/packageExports.ts
index 3307e55721..7fe6a49b35 100644
--- a/packages/cli/src/modules/migrate/commands/packageExports.ts
+++ b/packages/cli/src/modules/migrate/commands/packageExports.ts
@@ -18,7 +18,7 @@ import { cli } from 'cleye';
 import type { CommandContext } from '../../../wiring/types';
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
   throw new Error(
     'The `migrate package-exports` command has been removed, use `repo fix` instead.',
   );
diff --git a/packages/cli/src/modules/migrate/commands/packageLintConfigs.ts b/packages/cli/src/modules/migrate/commands/packageLintConfigs.ts
index c6839fe28b..73cbe380ec 100644
--- a/packages/cli/src/modules/migrate/commands/packageLintConfigs.ts
+++ b/packages/cli/src/modules/migrate/commands/packageLintConfigs.ts
@@ -24,7 +24,7 @@ import type { CommandContext } from '../../../wiring/types';
 const PREFIX = `module.exports = require('@backstage/cli/config/eslint-factory')`;
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
   const packages = await PackageGraph.listTargetPackages();
 
   const oldConfigs = [
diff --git a/packages/cli/src/modules/migrate/commands/packageRole.ts b/packages/cli/src/modules/migrate/commands/packageRole.ts
index 8d8c04b735..cc909a351c 100644
--- a/packages/cli/src/modules/migrate/commands/packageRole.ts
+++ b/packages/cli/src/modules/migrate/commands/packageRole.ts
@@ -23,7 +23,7 @@ import { targetPaths } from '@backstage/cli-common';
 import type { CommandContext } from '../../../wiring/types';
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
   const { packages } = await getPackages(targetPaths.dir);
 
   await Promise.all(
diff --git a/packages/cli/src/modules/migrate/commands/packageScripts.ts b/packages/cli/src/modules/migrate/commands/packageScripts.ts
index 0b7d9fc2ce..901cd8fc82 100644
--- a/packages/cli/src/modules/migrate/commands/packageScripts.ts
+++ b/packages/cli/src/modules/migrate/commands/packageScripts.ts
@@ -25,7 +25,7 @@ const configArgPattern = /--config[=\s][^\s$]+/;
 const noStartRoles: PackageRole[] = ['cli', 'common-library'];
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
   const packages = await PackageGraph.listTargetPackages();
 
   await Promise.all(
diff --git a/packages/cli/src/modules/migrate/commands/reactRouterDeps.ts b/packages/cli/src/modules/migrate/commands/reactRouterDeps.ts
index 702593c366..b2208e2dc4 100644
--- a/packages/cli/src/modules/migrate/commands/reactRouterDeps.ts
+++ b/packages/cli/src/modules/migrate/commands/reactRouterDeps.ts
@@ -24,7 +24,7 @@ const REACT_ROUTER_DEPS = ['react-router', 'react-router-dom'];
 const REACT_ROUTER_RANGE = '6.0.0-beta.0 || ^6.3.0';
 
 export default async ({ args, info }: CommandContext) => {
-  cli({ help: info }, undefined, args);
+  cli({ help: info, booleanFlagNegation: true }, undefined, args);
   const packages = await PackageGraph.listTargetPackages();
 
   await Promise.all(
diff --git a/packages/cli/src/modules/migrate/commands/versions/bump.ts b/packages/cli/src/modules/migrate/commands/versions/bump.ts
index a20cf1494a..8048c21505 100644
--- a/packages/cli/src/modules/migrate/commands/versions/bump.ts
+++ b/packages/cli/src/modules/migrate/commands/versions/bump.ts
@@ -80,6 +80,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         pattern: {
           type: String,
diff --git a/packages/cli/src/modules/migrate/commands/versions/migrate.ts b/packages/cli/src/modules/migrate/commands/versions/migrate.ts
index 4db800641a..1286af015e 100644
--- a/packages/cli/src/modules/migrate/commands/versions/migrate.ts
+++ b/packages/cli/src/modules/migrate/commands/versions/migrate.ts
@@ -45,6 +45,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         pattern: {
           type: String,
diff --git a/packages/cli/src/modules/new/commands/new.ts b/packages/cli/src/modules/new/commands/new.ts
index 082d0ca028..3769e19269 100644
--- a/packages/cli/src/modules/new/commands/new.ts
+++ b/packages/cli/src/modules/new/commands/new.ts
@@ -41,6 +41,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         select: {
           type: String,
diff --git a/packages/cli/src/modules/test/commands/repo/test.ts b/packages/cli/src/modules/test/commands/repo/test.ts
index c331caf994..1c39415192 100644
--- a/packages/cli/src/modules/test/commands/repo/test.ts
+++ b/packages/cli/src/modules/test/commands/repo/test.ts
@@ -147,6 +147,7 @@ export default async ({ args, info }: CommandContext) => {
   const { flags: opts } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         since: {
           type: String,
diff --git a/packages/cli/src/modules/translations/commands/export.ts b/packages/cli/src/modules/translations/commands/export.ts
index 4ee5658489..b6471f10f4 100644
--- a/packages/cli/src/modules/translations/commands/export.ts
+++ b/packages/cli/src/modules/translations/commands/export.ts
@@ -41,6 +41,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         output: {
           type: String,
diff --git a/packages/cli/src/modules/translations/commands/import.ts b/packages/cli/src/modules/translations/commands/import.ts
index 67b600b495..155724dd8c 100644
--- a/packages/cli/src/modules/translations/commands/import.ts
+++ b/packages/cli/src/modules/translations/commands/import.ts
@@ -47,6 +47,7 @@ export default async ({ args, info }: CommandContext) => {
   } = cli(
     {
       help: info,
+      booleanFlagNegation: true,
       flags: {
         input: {
           type: String,
diff --git a/yarn.lock b/yarn.lock
index 3dd82bf33e..f2b619e1a8 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -2893,7 +2893,7 @@ __metadata:
     buffer: "npm:^6.0.3"
     chalk: "npm:^4.0.0"
     chokidar: "npm:^3.3.1"
-    cleye: "npm:^2.2.1"
+    cleye: "npm:^2.3.0"
     commander: "npm:^14.0.3"
     cross-fetch: "npm:^4.0.0"
     cross-spawn: "npm:^7.0.3"
@@ -26903,7 +26903,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"cleye@npm:^2.2.1":
+"cleye@npm:^2.3.0":
   version: 2.3.0
   resolution: "cleye@npm:2.3.0"
   dependencies: