From aa655e1394c3bd1e88152468690dde31108b7b8e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 19:42:27 +0000
Subject: [PATCH 01/15] Initial plan


From b9e75f49be930778f191ded55404e04929838ba2 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 19:53:12 +0000
Subject: [PATCH 02/15] Add filtering for npm-incompatible properties in .npmrc
 syncing

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 .../rush-lib/src/cli/actions/PublishAction.ts |   4 +-
 libraries/rush-lib/src/scripts/install-run.ts |   8 +-
 libraries/rush-lib/src/utilities/Utilities.ts |   5 +-
 .../rush-lib/src/utilities/npmrcUtilities.ts  | 129 +++++++++++++-----
 .../src/utilities/test/npmrcUtilities.test.ts |  96 +++++++++++++
 5 files changed, 201 insertions(+), 41 deletions(-)

diff --git a/libraries/rush-lib/src/cli/actions/PublishAction.ts b/libraries/rush-lib/src/cli/actions/PublishAction.ts
index cb05204508..157d73dd41 100644
--- a/libraries/rush-lib/src/cli/actions/PublishAction.ts
+++ b/libraries/rush-lib/src/cli/actions/PublishAction.ts
@@ -593,7 +593,9 @@ export class PublishAction extends BaseRushAction {
       sourceNpmrcFolder: this.rushConfiguration.commonRushConfigFolder,
       targetNpmrcFolder: this._targetNpmrcPublishFolder,
       useNpmrcPublish: true,
-      supportEnvVarFallbackSyntax
+      supportEnvVarFallbackSyntax,
+      // Filter out npm-incompatible properties when using npm to publish
+      filterNpmIncompatibleProperties: true
     });
   }
 
diff --git a/libraries/rush-lib/src/scripts/install-run.ts b/libraries/rush-lib/src/scripts/install-run.ts
index 2aec0b67d1..7584ec01c8 100644
--- a/libraries/rush-lib/src/scripts/install-run.ts
+++ b/libraries/rush-lib/src/scripts/install-run.ts
@@ -173,7 +173,9 @@ function _resolvePackageVersion(
         sourceNpmrcFolder,
         targetNpmrcFolder: rushTempFolder,
         logger,
-        supportEnvVarFallbackSyntax: false
+        supportEnvVarFallbackSyntax: false,
+        // Filter out npm-incompatible properties when using npm
+        filterNpmIncompatibleProperties: true
       });
 
       // This returns something that looks like:
@@ -459,7 +461,9 @@ export function installAndRun(
       sourceNpmrcFolder,
       targetNpmrcFolder: packageInstallFolder,
       logger,
-      supportEnvVarFallbackSyntax: false
+      supportEnvVarFallbackSyntax: false,
+      // Filter out npm-incompatible properties when using npm
+      filterNpmIncompatibleProperties: true
     });
 
     _createPackageJson(packageInstallFolder, packageName, packageVersion);
diff --git a/libraries/rush-lib/src/utilities/Utilities.ts b/libraries/rush-lib/src/utilities/Utilities.ts
index c5fe8df92d..5b369286e7 100644
--- a/libraries/rush-lib/src/utilities/Utilities.ts
+++ b/libraries/rush-lib/src/utilities/Utilities.ts
@@ -531,7 +531,10 @@ export class Utilities {
       Utilities.syncNpmrc({
         sourceNpmrcFolder: commonRushConfigFolder,
         targetNpmrcFolder: directory,
-        supportEnvVarFallbackSyntax: false
+        supportEnvVarFallbackSyntax: false,
+        // Filter out npm-incompatible properties when using npm to install packages
+        // to avoid warnings about unknown config properties
+        filterNpmIncompatibleProperties: true
       });
     }
 
diff --git a/libraries/rush-lib/src/utilities/npmrcUtilities.ts b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
index b5a61e45af..102d3deea8 100644
--- a/libraries/rush-lib/src/utilities/npmrcUtilities.ts
+++ b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
@@ -25,10 +25,20 @@ const _combinedNpmrcMap: Map<string, string> = new Map();
 function _trimNpmrcFile(
   options: Pick<
     INpmrcTrimOptions,
-    'sourceNpmrcPath' | 'linesToAppend' | 'linesToPrepend' | 'supportEnvVarFallbackSyntax'
+    | 'sourceNpmrcPath'
+    | 'linesToAppend'
+    | 'linesToPrepend'
+    | 'supportEnvVarFallbackSyntax'
+    | 'filterNpmIncompatibleProperties'
   >
 ): string {
-  const { sourceNpmrcPath, linesToPrepend, linesToAppend, supportEnvVarFallbackSyntax } = options;
+  const {
+    sourceNpmrcPath,
+    linesToPrepend,
+    linesToAppend,
+    supportEnvVarFallbackSyntax,
+    filterNpmIncompatibleProperties
+  } = options;
   const combinedNpmrcFromCache: string | undefined = _combinedNpmrcMap.get(sourceNpmrcPath);
   if (combinedNpmrcFromCache !== undefined) {
     return combinedNpmrcFromCache;
@@ -49,7 +59,12 @@ function _trimNpmrcFile(
 
   npmrcFileLines = npmrcFileLines.map((line) => (line || '').trim());
 
-  const resultLines: string[] = trimNpmrcFileLines(npmrcFileLines, process.env, supportEnvVarFallbackSyntax);
+  const resultLines: string[] = trimNpmrcFileLines(
+    npmrcFileLines,
+    process.env,
+    supportEnvVarFallbackSyntax,
+    filterNpmIncompatibleProperties || false
+  );
 
   const combinedNpmrc: string = resultLines.join('\n');
 
@@ -59,17 +74,35 @@ function _trimNpmrcFile(
   return combinedNpmrc;
 }
 
+/**
+ * List of npmrc properties that are not supported by npm but may be present in the config.
+ * These include pnpm-specific properties and deprecated npm properties.
+ * Registry-scoped properties (starting with "//") are never filtered as they contain auth tokens.
+ */
+const NPM_INCOMPATIBLE_PROPERTIES: Set<string> = new Set([
+  // pnpm-specific hoisting configuration
+  'hoist',
+  'hoist-pattern',
+  'public-hoist-pattern',
+  'shamefully-hoist',
+  // Deprecated or unknown npm properties that cause warnings
+  'email',
+  'publish-branch'
+]);
+
 /**
  *
  * @param npmrcFileLines The npmrc file's lines
  * @param env The environment variables object
  * @param supportEnvVarFallbackSyntax Whether to support fallback values in the form of `${VAR_NAME:-fallback}`
+ * @param filterNpmIncompatibleProperties Whether to filter out properties that npm doesn't understand
  * @returns
  */
 export function trimNpmrcFileLines(
   npmrcFileLines: string[],
   env: NodeJS.ProcessEnv,
-  supportEnvVarFallbackSyntax: boolean
+  supportEnvVarFallbackSyntax: boolean,
+  filterNpmIncompatibleProperties: boolean = false
 ): string[] {
   const resultLines: string[] = [];
 
@@ -91,42 +124,62 @@ export function trimNpmrcFileLines(
 
     // Ignore comment lines
     if (!commentRegExp.test(line)) {
-      const environmentVariables: string[] | null = line.match(expansionRegExp);
-      if (environmentVariables) {
-        for (const token of environmentVariables) {
-          /**
-           * Remove the leading "${" and the trailing "}" from the token
-           *
-           * ${nameString}                  -> nameString
-           * ${nameString-fallbackString}   -> name-fallbackString
-           * ${nameString:-fallbackString}  -> name:-fallbackString
-           */
-          const nameWithFallback: string = token.substring(2, token.length - 1);
-
-          let environmentVariableName: string;
-          let fallback: string | undefined;
-          if (supportEnvVarFallbackSyntax) {
+      // Check if this is a property that npm doesn't understand
+      if (filterNpmIncompatibleProperties) {
+        // Extract the property name (everything before the '=' or '[')
+        const match: RegExpMatchArray | null = line.match(/^([^=\[]+)/);
+        if (match) {
+          const propertyName: string = match[1].trim();
+          
+          // Never filter registry-scoped properties (auth tokens, etc.)
+          // These start with "//" like "//registry.npmjs.org/:_authToken"
+          const isRegistryScoped: boolean = propertyName.startsWith('//');
+          
+          if (!isRegistryScoped && NPM_INCOMPATIBLE_PROPERTIES.has(propertyName)) {
+            lineShouldBeTrimmed = true;
+          }
+        }
+      }
+
+      // Check for undefined environment variables
+      if (!lineShouldBeTrimmed) {
+        const environmentVariables: string[] | null = line.match(expansionRegExp);
+        if (environmentVariables) {
+          for (const token of environmentVariables) {
             /**
-             * Get the environment variable name and fallback value.
+             * Remove the leading "${" and the trailing "}" from the token
              *
-             *                                name          fallback
-             * nameString                 ->  nameString    undefined
-             * nameString-fallbackString  ->  nameString    fallbackString
-             * nameString:-fallbackString ->  nameString    fallbackString
+             * ${nameString}                  -> nameString
+             * ${nameString-fallbackString}   -> name-fallbackString
+             * ${nameString:-fallbackString}  -> name:-fallbackString
              */
-            const matched: string[] | null = nameWithFallback.match(/^([^:-]+)(?:\:?-(.+))?$/);
-            // matched: [originStr, variableName, fallback]
-            environmentVariableName = matched?.[1] ?? nameWithFallback;
-            fallback = matched?.[2];
-          } else {
-            environmentVariableName = nameWithFallback;
-          }
-
-          // Is the environment variable and fallback value defined.
-          if (!env[environmentVariableName] && !fallback) {
-            // No, so trim this line
-            lineShouldBeTrimmed = true;
-            break;
+            const nameWithFallback: string = token.substring(2, token.length - 1);
+
+            let environmentVariableName: string;
+            let fallback: string | undefined;
+            if (supportEnvVarFallbackSyntax) {
+              /**
+               * Get the environment variable name and fallback value.
+               *
+               *                                name          fallback
+               * nameString                 ->  nameString    undefined
+               * nameString-fallbackString  ->  nameString    fallbackString
+               * nameString:-fallbackString ->  nameString    fallbackString
+               */
+              const matched: string[] | null = nameWithFallback.match(/^([^:-]+)(?:\:?-(.+))?$/);
+              // matched: [originStr, variableName, fallback]
+              environmentVariableName = matched?.[1] ?? nameWithFallback;
+              fallback = matched?.[2];
+            } else {
+              environmentVariableName = nameWithFallback;
+            }
+
+            // Is the environment variable and fallback value defined.
+            if (!env[environmentVariableName] && !fallback) {
+              // No, so trim this line
+              lineShouldBeTrimmed = true;
+              break;
+            }
           }
         }
       }
@@ -165,6 +218,7 @@ interface INpmrcTrimOptions {
   linesToPrepend?: string[];
   linesToAppend?: string[];
   supportEnvVarFallbackSyntax: boolean;
+  filterNpmIncompatibleProperties?: boolean;
 }
 
 function _copyAndTrimNpmrcFile(options: INpmrcTrimOptions): string {
@@ -197,6 +251,7 @@ export interface ISyncNpmrcOptions {
   linesToPrepend?: string[];
   linesToAppend?: string[];
   createIfMissing?: boolean;
+  filterNpmIncompatibleProperties?: boolean;
 }
 
 export function syncNpmrc(options: ISyncNpmrcOptions): string | undefined {
diff --git a/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts b/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
index b889435a0f..33ccbf1944 100644
--- a/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
+++ b/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
@@ -92,5 +92,101 @@ describe('npmrcUtilities', () => {
   describe(trimNpmrcFileLines.name, () => {
     describe('With support for env var fallback syntax', () => runTests(true));
     describe('Without support for env var fallback syntax', () => runTests(false));
+
+    describe('With npm-incompatible properties filtering', () => {
+      const supportEnvVarFallbackSyntax = false;
+      const filterNpmIncompatibleProperties = true;
+
+      it('filters out pnpm-specific hoisting properties', () => {
+        expect(
+          trimNpmrcFileLines(
+            [
+              'registry=https://registry.npmjs.org/',
+              'hoist=false',
+              'hoist-pattern[]=*eslint*',
+              'public-hoist-pattern[]=',
+              'shamefully-hoist=true',
+              'always-auth=false'
+            ],
+            {},
+            supportEnvVarFallbackSyntax,
+            filterNpmIncompatibleProperties
+          )
+        ).toMatchSnapshot();
+      });
+
+      it('filters out deprecated npm properties', () => {
+        expect(
+          trimNpmrcFileLines(
+            ['registry=https://registry.npmjs.org/', 'email=test@example.com', 'publish-branch=main'],
+            {},
+            supportEnvVarFallbackSyntax,
+            filterNpmIncompatibleProperties
+          )
+        ).toMatchSnapshot();
+      });
+
+      it('preserves registry-scoped auth tokens', () => {
+        expect(
+          trimNpmrcFileLines(
+            [
+              'registry=https://registry.npmjs.org/',
+              '//registry.npmjs.org/:_authToken=${NPM_TOKEN}',
+              '//my-registry.com/:_authToken=${MY_TOKEN}',
+              'email=test@example.com'
+            ],
+            { NPM_TOKEN: 'abc123', MY_TOKEN: 'xyz789' },
+            supportEnvVarFallbackSyntax,
+            filterNpmIncompatibleProperties
+          )
+        ).toMatchSnapshot();
+      });
+
+      it('preserves registry-scoped configurations', () => {
+        expect(
+          trimNpmrcFileLines(
+            [
+              'registry=https://registry.npmjs.org/',
+              '//registry.npmjs.org/:always-auth=true',
+              '//my-registry.com/:_authToken=${MY_TOKEN}',
+              'hoist=false'
+            ],
+            { MY_TOKEN: 'xyz789' },
+            supportEnvVarFallbackSyntax,
+            filterNpmIncompatibleProperties
+          )
+        ).toMatchSnapshot();
+      });
+
+      it('does not filter when filterNpmIncompatibleProperties is false', () => {
+        expect(
+          trimNpmrcFileLines(
+            ['registry=https://registry.npmjs.org/', 'email=test@example.com', 'hoist=false'],
+            {},
+            supportEnvVarFallbackSyntax,
+            false
+          )
+        ).toMatchSnapshot();
+      });
+
+      it('preserves standard npm properties', () => {
+        expect(
+          trimNpmrcFileLines(
+            [
+              'registry=https://registry.npmjs.org/',
+              'always-auth=false',
+              'strict-ssl=true',
+              'save-exact=true',
+              'package-lock=true',
+              'hoist=false',
+              'email=test@example.com'
+            ],
+            {},
+            supportEnvVarFallbackSyntax,
+            filterNpmIncompatibleProperties
+          )
+        ).toMatchSnapshot();
+      });
+    });
   });
 });

From f9e7b87ce2f70e22bb69a7051c9fd7d478078a2e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 20:01:04 +0000
Subject: [PATCH 03/15] Add test snapshots for npm-incompatible properties
 filtering

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 .../__snapshots__/npmrcUtilities.test.ts.snap | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap b/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
index 691864176a..e73c24d31d 100644
--- a/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
+++ b/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
@@ -1,5 +1,62 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
+exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering does not filter when filterNpmIncompatibleProperties is false 1`] = `
+Array [
+  "registry=https://registry.npmjs.org/",
+  "email=test@example.com",
+  "hoist=false",
+]
+`;
+
+exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering filters out deprecated npm properties 1`] = `
+Array [
+  "registry=https://registry.npmjs.org/",
+  "; MISSING ENVIRONMENT VARIABLE: email=test@example.com",
+  "; MISSING ENVIRONMENT VARIABLE: publish-branch=main",
+]
+`;
+
+exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering filters out pnpm-specific hoisting properties 1`] = `
+Array [
+  "registry=https://registry.npmjs.org/",
+  "; MISSING ENVIRONMENT VARIABLE: hoist=false",
+  "; MISSING ENVIRONMENT VARIABLE: hoist-pattern[]=*eslint*",
+  "; MISSING ENVIRONMENT VARIABLE: public-hoist-pattern[]=",
+  "; MISSING ENVIRONMENT VARIABLE: shamefully-hoist=true",
+  "always-auth=false",
+]
+`;
+
+exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering preserves registry-scoped auth tokens 1`] = `
+Array [
+  "registry=https://registry.npmjs.org/",
+  "//registry.npmjs.org/:_authToken=\${NPM_TOKEN}",
+  "//my-registry.com/:_authToken=\${MY_TOKEN}",
+  "; MISSING ENVIRONMENT VARIABLE: email=test@example.com",
+]
+`;
+
+exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering preserves registry-scoped configurations 1`] = `
+Array [
+  "registry=https://registry.npmjs.org/",
+  "//registry.npmjs.org/:always-auth=true",
+  "//my-registry.com/:_authToken=\${MY_TOKEN}",
+  "; MISSING ENVIRONMENT VARIABLE: hoist=false",
+]
+`;
+
+exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering preserves standard npm properties 1`] = `
+Array [
+  "registry=https://registry.npmjs.org/",
+  "always-auth=false",
+  "strict-ssl=true",
+  "save-exact=true",
+  "package-lock=true",
+  "; MISSING ENVIRONMENT VARIABLE: hoist=false",
+  "; MISSING ENVIRONMENT VARIABLE: email=test@example.com",
+]
+`;
+
 exports[`npmrcUtilities trimNpmrcFileLines With support for env var fallback syntax supports a a variable without a fallback 1`] = `
 Array [
   "; MISSING ENVIRONMENT VARIABLE: var1=\${foo}",

From 81f63c20e287fa1c3c37f3553c468e8bb73b1e5e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 20:03:35 +0000
Subject: [PATCH 04/15] Address code review feedback: improve regex pattern and
 add JSDoc return description

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 libraries/rush-lib/src/utilities/npmrcUtilities.ts | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/libraries/rush-lib/src/utilities/npmrcUtilities.ts b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
index 102d3deea8..a3dc9ad61b 100644
--- a/libraries/rush-lib/src/utilities/npmrcUtilities.ts
+++ b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
@@ -96,7 +96,7 @@ const NPM_INCOMPATIBLE_PROPERTIES: Set<string> = new Set([
  * @param env The environment variables object
  * @param supportEnvVarFallbackSyntax Whether to support fallback values in the form of `${VAR_NAME:-fallback}`
  * @param filterNpmIncompatibleProperties Whether to filter out properties that npm doesn't understand
- * @returns
+ * @returns An array of processed npmrc file lines with undefined environment variables and npm-incompatible properties commented out
  */
 export function trimNpmrcFileLines(
   npmrcFileLines: string[],
@@ -127,14 +127,14 @@ export function trimNpmrcFileLines(
       // Check if this is a property that npm doesn't understand
       if (filterNpmIncompatibleProperties) {
         // Extract the property name (everything before the '=' or '[')
-        const match: RegExpMatchArray | null = line.match(/^([^=\[]+)/);
+        const match: RegExpMatchArray | null = line.match(/^([^=\[\s]+)/);
         if (match) {
-          const propertyName: string = match[1].trim();
-          
+          const propertyName: string = match[1];
+
           // Never filter registry-scoped properties (auth tokens, etc.)
           // These start with "//" like "//registry.npmjs.org/:_authToken"
           const isRegistryScoped: boolean = propertyName.startsWith('//');
-          
+
           if (!isRegistryScoped && NPM_INCOMPATIBLE_PROPERTIES.has(propertyName)) {
             lineShouldBeTrimmed = true;
           }

From 6df696b0eb9cc3abed9e2a2db2dc1e17de1cba0c Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 20:05:59 +0000
Subject: [PATCH 05/15] Address code review nitpicks: extract regex constant
 and simplify boolean expression

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 libraries/rush-lib/src/utilities/npmrcUtilities.ts | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/libraries/rush-lib/src/utilities/npmrcUtilities.ts b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
index a3dc9ad61b..1d1551e535 100644
--- a/libraries/rush-lib/src/utilities/npmrcUtilities.ts
+++ b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
@@ -63,7 +63,7 @@ function _trimNpmrcFile(
     npmrcFileLines,
     process.env,
     supportEnvVarFallbackSyntax,
-    filterNpmIncompatibleProperties || false
+    filterNpmIncompatibleProperties
   );
 
   const combinedNpmrc: string = resultLines.join('\n');
@@ -90,6 +90,15 @@ const NPM_INCOMPATIBLE_PROPERTIES: Set<string> = new Set([
   'publish-branch'
 ]);
 
+/**
+ * Regular expression to extract property names from .npmrc lines.
+ * Matches everything before '=', '[', or whitespace to capture the property name.
+ * Examples:
+ *   "registry=https://..." -> matches "registry"
+ *   "hoist-pattern[]=..." -> matches "hoist-pattern"
+ */
+const PROPERTY_NAME_REGEX: RegExp = /^([^=\[\s]+)/;
+
 /**
  *
  * @param npmrcFileLines The npmrc file's lines
@@ -127,7 +136,7 @@ export function trimNpmrcFileLines(
       // Check if this is a property that npm doesn't understand
       if (filterNpmIncompatibleProperties) {
         // Extract the property name (everything before the '=' or '[')
-        const match: RegExpMatchArray | null = line.match(/^([^=\[\s]+)/);
+        const match: RegExpMatchArray | null = line.match(PROPERTY_NAME_REGEX);
         if (match) {
           const propertyName: string = match[1];
 

From 254a598dc721baa36cf39e28ba2bcda989dc1550 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 20:08:46 +0000
Subject: [PATCH 06/15] Improve error messages to distinguish npm-incompatible
 properties from missing env vars

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 .../rush-lib/src/utilities/npmrcUtilities.ts  | 16 ++++++++++++---
 .../__snapshots__/npmrcUtilities.test.ts.snap | 20 +++++++++----------
 2 files changed, 23 insertions(+), 13 deletions(-)

diff --git a/libraries/rush-lib/src/utilities/npmrcUtilities.ts b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
index 1d1551e535..49088a2997 100644
--- a/libraries/rush-lib/src/utilities/npmrcUtilities.ts
+++ b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
@@ -124,6 +124,7 @@ export function trimNpmrcFileLines(
   // Trim out lines that reference environment variables that aren't defined
   for (let line of npmrcFileLines) {
     let lineShouldBeTrimmed: boolean = false;
+    let trimReason: string = '';
 
     //remove spaces before or after key and value
     line = line
@@ -146,6 +147,7 @@ export function trimNpmrcFileLines(
 
           if (!isRegistryScoped && NPM_INCOMPATIBLE_PROPERTIES.has(propertyName)) {
             lineShouldBeTrimmed = true;
+            trimReason = 'NPM_INCOMPATIBLE_PROPERTY';
           }
         }
       }
@@ -187,6 +189,7 @@ export function trimNpmrcFileLines(
             if (!env[environmentVariableName] && !fallback) {
               // No, so trim this line
               lineShouldBeTrimmed = true;
+              trimReason = 'MISSING_ENVIRONMENT_VARIABLE';
               break;
             }
           }
@@ -195,9 +198,16 @@ export function trimNpmrcFileLines(
     }
 
     if (lineShouldBeTrimmed) {
-      // Example output:
-      // "; MISSING ENVIRONMENT VARIABLE: //my-registry.com/npm/:_authToken=${MY_AUTH_TOKEN}"
-      resultLines.push('; MISSING ENVIRONMENT VARIABLE: ' + line);
+      // Comment out the line with appropriate reason
+      if (trimReason === 'NPM_INCOMPATIBLE_PROPERTY') {
+        // Example output:
+        // "; UNSUPPORTED BY NPM: email=test@example.com"
+        resultLines.push('; UNSUPPORTED BY NPM: ' + line);
+      } else {
+        // Example output:
+        // "; MISSING ENVIRONMENT VARIABLE: //my-registry.com/npm/:_authToken=${MY_AUTH_TOKEN}"
+        resultLines.push('; MISSING ENVIRONMENT VARIABLE: ' + line);
+      }
     } else {
       resultLines.push(line);
     }
diff --git a/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap b/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
index e73c24d31d..5e4739c16f 100644
--- a/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
+++ b/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
@@ -11,18 +11,18 @@ Array [
 exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering filters out deprecated npm properties 1`] = `
 Array [
   "registry=https://registry.npmjs.org/",
-  "; MISSING ENVIRONMENT VARIABLE: email=test@example.com",
-  "; MISSING ENVIRONMENT VARIABLE: publish-branch=main",
+  "; UNSUPPORTED BY NPM: email=test@example.com",
+  "; UNSUPPORTED BY NPM: publish-branch=main",
 ]
 `;
 
 exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering filters out pnpm-specific hoisting properties 1`] = `
 Array [
   "registry=https://registry.npmjs.org/",
-  "; MISSING ENVIRONMENT VARIABLE: hoist=false",
-  "; MISSING ENVIRONMENT VARIABLE: hoist-pattern[]=*eslint*",
-  "; MISSING ENVIRONMENT VARIABLE: public-hoist-pattern[]=",
-  "; MISSING ENVIRONMENT VARIABLE: shamefully-hoist=true",
+  "; UNSUPPORTED BY NPM: hoist=false",
+  "; UNSUPPORTED BY NPM: hoist-pattern[]=*eslint*",
+  "; UNSUPPORTED BY NPM: public-hoist-pattern[]=",
+  "; UNSUPPORTED BY NPM: shamefully-hoist=true",
   "always-auth=false",
 ]
 `;
@@ -32,7 +32,7 @@ Array [
   "registry=https://registry.npmjs.org/",
   "//registry.npmjs.org/:_authToken=\${NPM_TOKEN}",
   "//my-registry.com/:_authToken=\${MY_TOKEN}",
-  "; MISSING ENVIRONMENT VARIABLE: email=test@example.com",
+  "; UNSUPPORTED BY NPM: email=test@example.com",
 ]
 `;
 
@@ -41,7 +41,7 @@ Array [
   "registry=https://registry.npmjs.org/",
   "//registry.npmjs.org/:always-auth=true",
   "//my-registry.com/:_authToken=\${MY_TOKEN}",
-  "; MISSING ENVIRONMENT VARIABLE: hoist=false",
+  "; UNSUPPORTED BY NPM: hoist=false",
 ]
 `;
 
@@ -52,8 +52,8 @@ Array [
   "strict-ssl=true",
   "save-exact=true",
   "package-lock=true",
-  "; MISSING ENVIRONMENT VARIABLE: hoist=false",
-  "; MISSING ENVIRONMENT VARIABLE: email=test@example.com",
+  "; UNSUPPORTED BY NPM: hoist=false",
+  "; UNSUPPORTED BY NPM: email=test@example.com",
 ]
 `;
 

From 1d0acaa8193b090e4a5f13611ed99f0bb467cd0b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 20:15:27 +0000
Subject: [PATCH 07/15] Fix TypeScript error in isVariableSetInNpmrcFile and
 update test typo

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 .../rush-lib/src/utilities/npmrcUtilities.ts  |  6 ++-
 .../__snapshots__/npmrcUtilities.test.ts.snap | 48 +++++++++----------
 .../src/utilities/test/npmrcUtilities.test.ts |  2 +-
 3 files changed, 30 insertions(+), 26 deletions(-)

diff --git a/libraries/rush-lib/src/utilities/npmrcUtilities.ts b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
index 49088a2997..4501a98853 100644
--- a/libraries/rush-lib/src/utilities/npmrcUtilities.ts
+++ b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
@@ -326,7 +326,11 @@ export function isVariableSetInNpmrcFile(
     return false;
   }
 
-  const trimmedNpmrcFile: string = _trimNpmrcFile({ sourceNpmrcPath, supportEnvVarFallbackSyntax });
+  const trimmedNpmrcFile: string = _trimNpmrcFile({
+    sourceNpmrcPath,
+    supportEnvVarFallbackSyntax,
+    filterNpmIncompatibleProperties: false
+  });
 
   const variableKeyRegExp: RegExp = new RegExp(`^${variableKey}=`, 'm');
   return trimmedNpmrcFile.match(variableKeyRegExp) !== null;
diff --git a/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap b/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
index 5e4739c16f..4df9d2ea68 100644
--- a/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
+++ b/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
@@ -57,18 +57,6 @@ Array [
 ]
 `;
 
-exports[`npmrcUtilities trimNpmrcFileLines With support for env var fallback syntax supports a a variable without a fallback 1`] = `
-Array [
-  "; MISSING ENVIRONMENT VARIABLE: var1=\${foo}",
-]
-`;
-
-exports[`npmrcUtilities trimNpmrcFileLines With support for env var fallback syntax supports a a variable without a fallback 2`] = `
-Array [
-  "var1=\${foo}",
-]
-`;
-
 exports[`npmrcUtilities trimNpmrcFileLines With support for env var fallback syntax supports a variable with a fallback 1`] = `
 Array [
   "var1=\${foo-fallback_value}",
@@ -117,6 +105,18 @@ Array [
 ]
 `;
 
+exports[`npmrcUtilities trimNpmrcFileLines With support for env var fallback syntax supports a variable without a fallback 1`] = `
+Array [
+  "; MISSING ENVIRONMENT VARIABLE: var1=\${foo}",
+]
+`;
+
+exports[`npmrcUtilities trimNpmrcFileLines With support for env var fallback syntax supports a variable without a fallback 2`] = `
+Array [
+  "var1=\${foo}",
+]
+`;
+
 exports[`npmrcUtilities trimNpmrcFileLines With support for env var fallback syntax supports malformed lines 1`] = `
 Array [
   "; MISSING ENVIRONMENT VARIABLE: var1=\${foo_fallback_value}",
@@ -169,18 +169,6 @@ Array [
 ]
 `;
 
-exports[`npmrcUtilities trimNpmrcFileLines Without support for env var fallback syntax supports a a variable without a fallback 1`] = `
-Array [
-  "; MISSING ENVIRONMENT VARIABLE: var1=\${foo}",
-]
-`;
-
-exports[`npmrcUtilities trimNpmrcFileLines Without support for env var fallback syntax supports a a variable without a fallback 2`] = `
-Array [
-  "var1=\${foo}",
-]
-`;
-
 exports[`npmrcUtilities trimNpmrcFileLines Without support for env var fallback syntax supports a variable with a fallback 1`] = `
 Array [
   "; MISSING ENVIRONMENT VARIABLE: var1=\${foo-fallback_value}",
@@ -229,6 +217,18 @@ Array [
 ]
 `;
 
+exports[`npmrcUtilities trimNpmrcFileLines Without support for env var fallback syntax supports a variable without a fallback 1`] = `
+Array [
+  "; MISSING ENVIRONMENT VARIABLE: var1=\${foo}",
+]
+`;
+
+exports[`npmrcUtilities trimNpmrcFileLines Without support for env var fallback syntax supports a variable without a fallback 2`] = `
+Array [
+  "var1=\${foo}",
+]
+`;
+
 exports[`npmrcUtilities trimNpmrcFileLines Without support for env var fallback syntax supports malformed lines 1`] = `
 Array [
   "; MISSING ENVIRONMENT VARIABLE: var1=\${foo_fallback_value}",
diff --git a/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts b/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
index 33ccbf1944..9db4f00102 100644
--- a/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
+++ b/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
@@ -9,7 +9,7 @@ describe('npmrcUtilities', () => {
       expect(trimNpmrcFileLines([], {}, supportEnvVarFallbackSyntax)).toEqual([]);
     });
 
-    it('supports a a variable without a fallback', () => {
+    it('supports a variable without a fallback', () => {
       expect(trimNpmrcFileLines(['var1=${foo}'], {}, supportEnvVarFallbackSyntax)).toMatchSnapshot();
       expect(
         trimNpmrcFileLines(['var1=${foo}'], { foo: 'test' }, supportEnvVarFallbackSyntax)

From 86ce5b5a181895674d0334772e64940c7ddd0519 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 20:17:32 +0000
Subject: [PATCH 08/15] Add documentation comment explaining why regex 'g' flag
 is omitted

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 libraries/rush-lib/src/utilities/npmrcUtilities.ts | 1 +
 1 file changed, 1 insertion(+)

diff --git a/libraries/rush-lib/src/utilities/npmrcUtilities.ts b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
index 4501a98853..aaa4088d3b 100644
--- a/libraries/rush-lib/src/utilities/npmrcUtilities.ts
+++ b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
@@ -93,6 +93,7 @@ const NPM_INCOMPATIBLE_PROPERTIES: Set<string> = new Set([
 /**
  * Regular expression to extract property names from .npmrc lines.
  * Matches everything before '=', '[', or whitespace to capture the property name.
+ * Note: The 'g' flag is intentionally omitted since we only need the first match.
  * Examples:
  *   "registry=https://..." -> matches "registry"
  *   "hoist-pattern[]=..." -> matches "hoist-pattern"

From 13cf88d99ab5235a14ca257337375483ff3a1225 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 21:31:19 +0000
Subject: [PATCH 09/15] Only filter npm-incompatible properties when not using
 pnpm for publishing

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 libraries/rush-lib/src/cli/actions/PublishAction.ts | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/libraries/rush-lib/src/cli/actions/PublishAction.ts b/libraries/rush-lib/src/cli/actions/PublishAction.ts
index 157d73dd41..0e250e1963 100644
--- a/libraries/rush-lib/src/cli/actions/PublishAction.ts
+++ b/libraries/rush-lib/src/cli/actions/PublishAction.ts
@@ -594,8 +594,9 @@ export class PublishAction extends BaseRushAction {
       targetNpmrcFolder: this._targetNpmrcPublishFolder,
       useNpmrcPublish: true,
       supportEnvVarFallbackSyntax,
-      // Filter out npm-incompatible properties when using npm to publish
-      filterNpmIncompatibleProperties: true
+      // Filter out npm-incompatible properties when using npm or yarn to publish.
+      // Don't filter for pnpm since it understands pnpm-specific properties.
+      filterNpmIncompatibleProperties: !this.rushConfiguration.isPnpm
     });
   }
 

From 2e01c52118db430dd9b2b79cec5b21df762d220e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 21:47:53 +0000
Subject: [PATCH 10/15] Only filter npmrc properties when repo uses pnpm/yarn,
 not when repo uses npm

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 .../logic/installManager/InstallHelpers.ts    |  5 +++-
 libraries/rush-lib/src/scripts/install-run.ts | 28 ++++++++++++++++---
 libraries/rush-lib/src/utilities/Utilities.ts | 15 +++++++---
 3 files changed, 39 insertions(+), 9 deletions(-)

diff --git a/libraries/rush-lib/src/logic/installManager/InstallHelpers.ts b/libraries/rush-lib/src/logic/installManager/InstallHelpers.ts
index 35a1998c6a..515f9e5bec 100644
--- a/libraries/rush-lib/src/logic/installManager/InstallHelpers.ts
+++ b/libraries/rush-lib/src/logic/installManager/InstallHelpers.ts
@@ -257,7 +257,10 @@ export class InstallHelpers {
         // In particular, we'll assume that two different NPM registries cannot have two
         // different implementations of the same version of the same package.
         // This was needed for: https://github.com/microsoft/rushstack/issues/691
-        commonRushConfigFolder: rushConfiguration.commonRushConfigFolder
+        commonRushConfigFolder: rushConfiguration.commonRushConfigFolder,
+        // Only filter npm-incompatible properties when the repo uses pnpm or yarn.
+        // If the repo uses npm, the .npmrc is already configured for npm, so don't filter.
+        filterNpmIncompatibleProperties: rushConfiguration.packageManager !== 'npm'
       });
 
       logIfConsoleOutputIsNotRestricted(
diff --git a/libraries/rush-lib/src/scripts/install-run.ts b/libraries/rush-lib/src/scripts/install-run.ts
index 7584ec01c8..adaa5fcde3 100644
--- a/libraries/rush-lib/src/scripts/install-run.ts
+++ b/libraries/rush-lib/src/scripts/install-run.ts
@@ -124,6 +124,23 @@ function _getRushTempFolder(rushCommonFolder: string): string {
   }
 }
 
+/**
+ * Check if the Rush repository is configured to use npm as the package manager.
+ * Returns true if the repo uses npm, false for pnpm or yarn.
+ */
+function _isRepoUsingNpm(rushJsonFolder: string): boolean {
+  try {
+    const rushJsonPath: string = path.join(rushJsonFolder, RUSH_JSON_FILENAME);
+    const rushJsonContent: string = fs.readFileSync(rushJsonPath, 'utf-8');
+    const rushJson: { packageManager?: string } = JSON.parse(rushJsonContent);
+    // If packageManager is not specified or is 'npm', return true
+    return !rushJson.packageManager || rushJson.packageManager === 'npm';
+  } catch (e) {
+    // If we can't read rush.json, assume npm (conservative default)
+    return true;
+  }
+}
+
 export interface IPackageSpecifier {
   name: string;
   version: string | undefined;
@@ -168,14 +185,16 @@ function _resolvePackageVersion(
     try {
       const rushTempFolder: string = _getRushTempFolder(rushCommonFolder);
       const sourceNpmrcFolder: string = path.join(rushCommonFolder, 'config', 'rush');
+      const rushJsonFolder: string = findRushJsonFolder();
 
       syncNpmrc({
         sourceNpmrcFolder,
         targetNpmrcFolder: rushTempFolder,
         logger,
         supportEnvVarFallbackSyntax: false,
-        // Filter out npm-incompatible properties when using npm
-        filterNpmIncompatibleProperties: true
+        // Only filter npm-incompatible properties when the repo uses pnpm or yarn.
+        // If the repo uses npm, the .npmrc is already configured for npm, so don't filter.
+        filterNpmIncompatibleProperties: !_isRepoUsingNpm(rushJsonFolder)
       });
 
       // This returns something that looks like:
@@ -462,8 +481,9 @@ export function installAndRun(
       targetNpmrcFolder: packageInstallFolder,
       logger,
       supportEnvVarFallbackSyntax: false,
-      // Filter out npm-incompatible properties when using npm
-      filterNpmIncompatibleProperties: true
+      // Only filter npm-incompatible properties when the repo uses pnpm or yarn.
+      // If the repo uses npm, the .npmrc is already configured for npm, so don't filter.
+      filterNpmIncompatibleProperties: !_isRepoUsingNpm(rushJsonFolder)
     });
 
     _createPackageJson(packageInstallFolder, packageName, packageVersion);
diff --git a/libraries/rush-lib/src/utilities/Utilities.ts b/libraries/rush-lib/src/utilities/Utilities.ts
index 5b369286e7..a3ab86e1a2 100644
--- a/libraries/rush-lib/src/utilities/Utilities.ts
+++ b/libraries/rush-lib/src/utilities/Utilities.ts
@@ -65,6 +65,12 @@ export interface IInstallPackageInDirectoryOptions {
   maxInstallAttempts: number;
   commonRushConfigFolder: string | undefined;
   suppressOutput?: boolean;
+  /**
+   * Whether to filter npm-incompatible properties from .npmrc.
+   * This should be true when the .npmrc is configured for a different package manager (pnpm/yarn)
+   * but npm is being used to install packages.
+   */
+  filterNpmIncompatibleProperties?: boolean;
 }
 
 export interface ILifecycleCommandOptions {
@@ -505,7 +511,8 @@ export class Utilities {
     commonRushConfigFolder,
     maxInstallAttempts,
     suppressOutput,
-    directory
+    directory,
+    filterNpmIncompatibleProperties
   }: IInstallPackageInDirectoryOptions): Promise<void> {
     directory = path.resolve(directory);
     const directoryExists: boolean = await FileSystem.existsAsync(directory);
@@ -532,9 +539,9 @@ export class Utilities {
         sourceNpmrcFolder: commonRushConfigFolder,
         targetNpmrcFolder: directory,
         supportEnvVarFallbackSyntax: false,
-        // Filter out npm-incompatible properties when using npm to install packages
-        // to avoid warnings about unknown config properties
-        filterNpmIncompatibleProperties: true
+        // Filter out npm-incompatible properties only when the .npmrc is configured for
+        // a different package manager (pnpm/yarn) but npm is being used to install.
+        filterNpmIncompatibleProperties: filterNpmIncompatibleProperties || false
       });
     }
 

From 44381bb138413b8b119998382b473a8b6284efa4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 23:12:40 +0000
Subject: [PATCH 11/15] Address code review feedback: simplify filtering logic
 and add changelog

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 ...ter-npmrc-properties_2026-01-26-23-12.json | 11 +++++++
 .../rush-lib/src/cli/actions/PublishAction.ts |  2 +-
 libraries/rush-lib/src/scripts/install-run.ts | 30 ++++---------------
 libraries/rush-lib/src/utilities/Utilities.ts |  4 +--
 4 files changed, 20 insertions(+), 27 deletions(-)
 create mode 100644 common/changes/@microsoft/rush-lib/filter-npmrc-properties_2026-01-26-23-12.json

diff --git a/common/changes/@microsoft/rush-lib/filter-npmrc-properties_2026-01-26-23-12.json b/common/changes/@microsoft/rush-lib/filter-npmrc-properties_2026-01-26-23-12.json
new file mode 100644
index 0000000000..c4c68f25c6
--- /dev/null
+++ b/common/changes/@microsoft/rush-lib/filter-npmrc-properties_2026-01-26-23-12.json
@@ -0,0 +1,11 @@
+{
+  "changes": [
+    {
+      "comment": "Filter npm-incompatible properties from .npmrc when npm is used with a configuration intended for pnpm or yarn, to eliminate spurious warnings during package manager installation.",
+      "type": "patch",
+      "packageName": "@microsoft/rush-lib"
+    }
+  ],
+  "packageName": "@microsoft/rush-lib",
+  "email": "copilot@github.com"
+}
diff --git a/libraries/rush-lib/src/cli/actions/PublishAction.ts b/libraries/rush-lib/src/cli/actions/PublishAction.ts
index 0e250e1963..6e36e2f180 100644
--- a/libraries/rush-lib/src/cli/actions/PublishAction.ts
+++ b/libraries/rush-lib/src/cli/actions/PublishAction.ts
@@ -596,7 +596,7 @@ export class PublishAction extends BaseRushAction {
       supportEnvVarFallbackSyntax,
       // Filter out npm-incompatible properties when using npm or yarn to publish.
       // Don't filter for pnpm since it understands pnpm-specific properties.
-      filterNpmIncompatibleProperties: !this.rushConfiguration.isPnpm
+      filterNpmIncompatibleProperties: this.rushConfiguration.packageManager !== 'pnpm'
     });
   }
 
diff --git a/libraries/rush-lib/src/scripts/install-run.ts b/libraries/rush-lib/src/scripts/install-run.ts
index adaa5fcde3..7f56856648 100644
--- a/libraries/rush-lib/src/scripts/install-run.ts
+++ b/libraries/rush-lib/src/scripts/install-run.ts
@@ -124,23 +124,6 @@ function _getRushTempFolder(rushCommonFolder: string): string {
   }
 }
 
-/**
- * Check if the Rush repository is configured to use npm as the package manager.
- * Returns true if the repo uses npm, false for pnpm or yarn.
- */
-function _isRepoUsingNpm(rushJsonFolder: string): boolean {
-  try {
-    const rushJsonPath: string = path.join(rushJsonFolder, RUSH_JSON_FILENAME);
-    const rushJsonContent: string = fs.readFileSync(rushJsonPath, 'utf-8');
-    const rushJson: { packageManager?: string } = JSON.parse(rushJsonContent);
-    // If packageManager is not specified or is 'npm', return true
-    return !rushJson.packageManager || rushJson.packageManager === 'npm';
-  } catch (e) {
-    // If we can't read rush.json, assume npm (conservative default)
-    return true;
-  }
-}
-
 export interface IPackageSpecifier {
   name: string;
   version: string | undefined;
@@ -185,16 +168,15 @@ function _resolvePackageVersion(
     try {
       const rushTempFolder: string = _getRushTempFolder(rushCommonFolder);
       const sourceNpmrcFolder: string = path.join(rushCommonFolder, 'config', 'rush');
-      const rushJsonFolder: string = findRushJsonFolder();
 
       syncNpmrc({
         sourceNpmrcFolder,
         targetNpmrcFolder: rushTempFolder,
         logger,
         supportEnvVarFallbackSyntax: false,
-        // Only filter npm-incompatible properties when the repo uses pnpm or yarn.
-        // If the repo uses npm, the .npmrc is already configured for npm, so don't filter.
-        filterNpmIncompatibleProperties: !_isRepoUsingNpm(rushJsonFolder)
+        // Always filter npm-incompatible properties in install-run scripts.
+        // Any warnings will be shown when running Rush commands directly.
+        filterNpmIncompatibleProperties: true
       });
 
       // This returns something that looks like:
@@ -481,9 +463,9 @@ export function installAndRun(
       targetNpmrcFolder: packageInstallFolder,
       logger,
       supportEnvVarFallbackSyntax: false,
-      // Only filter npm-incompatible properties when the repo uses pnpm or yarn.
-      // If the repo uses npm, the .npmrc is already configured for npm, so don't filter.
-      filterNpmIncompatibleProperties: !_isRepoUsingNpm(rushJsonFolder)
+      // Always filter npm-incompatible properties in install-run scripts.
+      // Any warnings will be shown when running Rush commands directly.
+      filterNpmIncompatibleProperties: true
     });
 
     _createPackageJson(packageInstallFolder, packageName, packageVersion);
diff --git a/libraries/rush-lib/src/utilities/Utilities.ts b/libraries/rush-lib/src/utilities/Utilities.ts
index a3ab86e1a2..6c502224ef 100644
--- a/libraries/rush-lib/src/utilities/Utilities.ts
+++ b/libraries/rush-lib/src/utilities/Utilities.ts
@@ -512,7 +512,7 @@ export class Utilities {
     maxInstallAttempts,
     suppressOutput,
     directory,
-    filterNpmIncompatibleProperties
+    filterNpmIncompatibleProperties = false
   }: IInstallPackageInDirectoryOptions): Promise<void> {
     directory = path.resolve(directory);
     const directoryExists: boolean = await FileSystem.existsAsync(directory);
@@ -541,7 +541,7 @@ export class Utilities {
         supportEnvVarFallbackSyntax: false,
         // Filter out npm-incompatible properties only when the .npmrc is configured for
         // a different package manager (pnpm/yarn) but npm is being used to install.
-        filterNpmIncompatibleProperties: filterNpmIncompatibleProperties || false
+        filterNpmIncompatibleProperties
       });
     }
 

From bbc2d666808d8e2729f05ab2da73943c8c05a964 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 23:31:54 +0000
Subject: [PATCH 12/15] Always filter npmrc in publish and fix changelog for
 lockstepped versioning

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 .../rush-lib/filter-npmrc-properties_2026-01-26-23-12.json  | 6 +++---
 libraries/rush-lib/src/cli/actions/PublishAction.ts         | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/common/changes/@microsoft/rush-lib/filter-npmrc-properties_2026-01-26-23-12.json b/common/changes/@microsoft/rush-lib/filter-npmrc-properties_2026-01-26-23-12.json
index c4c68f25c6..54bb3a29b1 100644
--- a/common/changes/@microsoft/rush-lib/filter-npmrc-properties_2026-01-26-23-12.json
+++ b/common/changes/@microsoft/rush-lib/filter-npmrc-properties_2026-01-26-23-12.json
@@ -2,10 +2,10 @@
   "changes": [
     {
       "comment": "Filter npm-incompatible properties from .npmrc when npm is used with a configuration intended for pnpm or yarn, to eliminate spurious warnings during package manager installation.",
-      "type": "patch",
-      "packageName": "@microsoft/rush-lib"
+      "type": "none",
+      "packageName": "@microsoft/rush"
     }
   ],
-  "packageName": "@microsoft/rush-lib",
+  "packageName": "@microsoft/rush",
   "email": "copilot@github.com"
 }
diff --git a/libraries/rush-lib/src/cli/actions/PublishAction.ts b/libraries/rush-lib/src/cli/actions/PublishAction.ts
index 6e36e2f180..796d0c21b3 100644
--- a/libraries/rush-lib/src/cli/actions/PublishAction.ts
+++ b/libraries/rush-lib/src/cli/actions/PublishAction.ts
@@ -594,9 +594,9 @@ export class PublishAction extends BaseRushAction {
       targetNpmrcFolder: this._targetNpmrcPublishFolder,
       useNpmrcPublish: true,
       supportEnvVarFallbackSyntax,
-      // Filter out npm-incompatible properties when using npm or yarn to publish.
-      // Don't filter for pnpm since it understands pnpm-specific properties.
-      filterNpmIncompatibleProperties: this.rushConfiguration.packageManager !== 'pnpm'
+      // Always filter npm-incompatible properties when publishing.
+      // The .npmrc-publish file may contain pnpm-specific properties even in npm repos.
+      filterNpmIncompatibleProperties: true
     });
   }
 

From b92cf31ab90e0548e3ccdd06d7b29f87dd53f755 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 26 Jan 2026 23:48:16 +0000
Subject: [PATCH 13/15] Remove filtering from PublishAction - only filter in
 install-run and installPackageInDirectoryAsync

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 libraries/rush-lib/src/cli/actions/PublishAction.ts | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/libraries/rush-lib/src/cli/actions/PublishAction.ts b/libraries/rush-lib/src/cli/actions/PublishAction.ts
index 796d0c21b3..cb05204508 100644
--- a/libraries/rush-lib/src/cli/actions/PublishAction.ts
+++ b/libraries/rush-lib/src/cli/actions/PublishAction.ts
@@ -593,10 +593,7 @@ export class PublishAction extends BaseRushAction {
       sourceNpmrcFolder: this.rushConfiguration.commonRushConfigFolder,
       targetNpmrcFolder: this._targetNpmrcPublishFolder,
       useNpmrcPublish: true,
-      supportEnvVarFallbackSyntax,
-      // Always filter npm-incompatible properties when publishing.
-      // The .npmrc-publish file may contain pnpm-specific properties even in npm repos.
-      filterNpmIncompatibleProperties: true
+      supportEnvVarFallbackSyntax
     });
   }
 

From 383d111f30fd55f0102b974686681f5a38a0471b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 27 Jan 2026 00:12:38 +0000
Subject: [PATCH 14/15] Filter pnpm-specific registry-scoped properties
 (tokenHelper, urlTokenHelper)

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 .../rush-lib/src/utilities/npmrcUtilities.ts  | 35 +++++++++++++++----
 .../__snapshots__/npmrcUtilities.test.ts.snap | 10 ++++++
 .../src/utilities/test/npmrcUtilities.test.ts | 17 +++++++++
 3 files changed, 56 insertions(+), 6 deletions(-)

diff --git a/libraries/rush-lib/src/utilities/npmrcUtilities.ts b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
index aaa4088d3b..adf1f851d1 100644
--- a/libraries/rush-lib/src/utilities/npmrcUtilities.ts
+++ b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
@@ -77,7 +77,6 @@ function _trimNpmrcFile(
 /**
  * List of npmrc properties that are not supported by npm but may be present in the config.
  * These include pnpm-specific properties and deprecated npm properties.
- * Registry-scoped properties (starting with "//") are never filtered as they contain auth tokens.
  */
 const NPM_INCOMPATIBLE_PROPERTIES: Set<string> = new Set([
   // pnpm-specific hoisting configuration
@@ -90,6 +89,17 @@ const NPM_INCOMPATIBLE_PROPERTIES: Set<string> = new Set([
   'publish-branch'
 ]);
 
+/**
+ * List of registry-scoped npmrc property suffixes that are pnpm-specific.
+ * These are properties like "//registry.example.com/:tokenHelper" where "tokenHelper"
+ * is the suffix after the last colon.
+ */
+const NPM_INCOMPATIBLE_REGISTRY_SCOPED_PROPERTIES: Set<string> = new Set([
+  // pnpm-specific token helper properties
+  'tokenHelper',
+  'urlTokenHelper'
+]);
+
 /**
  * Regular expression to extract property names from .npmrc lines.
  * Matches everything before '=', '[', or whitespace to capture the property name.
@@ -142,13 +152,26 @@ export function trimNpmrcFileLines(
         if (match) {
           const propertyName: string = match[1];
 
-          // Never filter registry-scoped properties (auth tokens, etc.)
-          // These start with "//" like "//registry.npmjs.org/:_authToken"
+          // Check if this is a registry-scoped property (starts with "//" like "//registry.npmjs.org/:_authToken")
           const isRegistryScoped: boolean = propertyName.startsWith('//');
 
-          if (!isRegistryScoped && NPM_INCOMPATIBLE_PROPERTIES.has(propertyName)) {
-            lineShouldBeTrimmed = true;
-            trimReason = 'NPM_INCOMPATIBLE_PROPERTY';
+          if (isRegistryScoped) {
+            // For registry-scoped properties, check if the suffix (after the last colon) is npm-incompatible
+            // Example: "//registry.example.com/:tokenHelper" -> suffix is "tokenHelper"
+            const lastColonIndex: number = propertyName.lastIndexOf(':');
+            if (lastColonIndex !== -1) {
+              const registryPropertySuffix: string = propertyName.substring(lastColonIndex + 1);
+              if (NPM_INCOMPATIBLE_REGISTRY_SCOPED_PROPERTIES.has(registryPropertySuffix)) {
+                lineShouldBeTrimmed = true;
+                trimReason = 'NPM_INCOMPATIBLE_PROPERTY';
+              }
+            }
+          } else {
+            // For non-registry-scoped properties, check the full property name
+            if (NPM_INCOMPATIBLE_PROPERTIES.has(propertyName)) {
+              lineShouldBeTrimmed = true;
+              trimReason = 'NPM_INCOMPATIBLE_PROPERTY';
+            }
           }
         }
       }
diff --git a/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap b/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
index 4df9d2ea68..0484645555 100644
--- a/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
+++ b/libraries/rush-lib/src/utilities/test/__snapshots__/npmrcUtilities.test.ts.snap
@@ -27,6 +27,16 @@ Array [
 ]
 `;
 
+exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering filters out pnpm-specific registry-scoped properties 1`] = `
+Array [
+  "registry=https://registry.npmjs.org/",
+  "//registry.npmjs.org/:_authToken=\${NPM_TOKEN}",
+  "; UNSUPPORTED BY NPM: //my-registry.com/:tokenHelper=/path/to/helper",
+  "; UNSUPPORTED BY NPM: //other-registry.com/:urlTokenHelper=/path/to/url-helper",
+  "//registry.npmjs.org/:always-auth=true",
+]
+`;
+
 exports[`npmrcUtilities trimNpmrcFileLines With npm-incompatible properties filtering preserves registry-scoped auth tokens 1`] = `
 Array [
   "registry=https://registry.npmjs.org/",
diff --git a/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts b/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
index 9db4f00102..3c84a54cfc 100644
--- a/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
+++ b/libraries/rush-lib/src/utilities/test/npmrcUtilities.test.ts
@@ -187,6 +187,23 @@ describe('npmrcUtilities', () => {
           )
         ).toMatchSnapshot();
       });
+
+      it('filters out pnpm-specific registry-scoped properties', () => {
+        expect(
+          trimNpmrcFileLines(
+            [
+              'registry=https://registry.npmjs.org/',
+              '//registry.npmjs.org/:_authToken=${NPM_TOKEN}',
+              '//my-registry.com/:tokenHelper=/path/to/helper',
+              '//other-registry.com/:urlTokenHelper=/path/to/url-helper',
+              '//registry.npmjs.org/:always-auth=true'
+            ],
+            { NPM_TOKEN: 'abc123' },
+            supportEnvVarFallbackSyntax,
+            filterNpmIncompatibleProperties
+          )
+        ).toMatchSnapshot();
+      });
     });
   });
 });

From 1300bc85c4feb02b5132d82413bfd3de506aa185 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 27 Jan 2026 00:23:32 +0000
Subject: [PATCH 15/15] Address @dmichon-msft feedback: make env configurable,
 use slice, and named regex groups

Co-authored-by: iclanton <5010588+iclanton@users.noreply.github.com>
---
 .../rush-lib/src/utilities/npmrcUtilities.ts  | 26 ++++++++++++++-----
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/libraries/rush-lib/src/utilities/npmrcUtilities.ts b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
index adf1f851d1..6e5b1da615 100644
--- a/libraries/rush-lib/src/utilities/npmrcUtilities.ts
+++ b/libraries/rush-lib/src/utilities/npmrcUtilities.ts
@@ -30,6 +30,7 @@ function _trimNpmrcFile(
     | 'linesToPrepend'
     | 'supportEnvVarFallbackSyntax'
     | 'filterNpmIncompatibleProperties'
+    | 'env'
   >
 ): string {
   const {
@@ -37,7 +38,8 @@ function _trimNpmrcFile(
     linesToPrepend,
     linesToAppend,
     supportEnvVarFallbackSyntax,
-    filterNpmIncompatibleProperties
+    filterNpmIncompatibleProperties,
+    env = process.env
   } = options;
   const combinedNpmrcFromCache: string | undefined = _combinedNpmrcMap.get(sourceNpmrcPath);
   if (combinedNpmrcFromCache !== undefined) {
@@ -61,7 +63,7 @@ function _trimNpmrcFile(
 
   const resultLines: string[] = trimNpmrcFileLines(
     npmrcFileLines,
-    process.env,
+    env,
     supportEnvVarFallbackSyntax,
     filterNpmIncompatibleProperties
   );
@@ -110,6 +112,15 @@ const NPM_INCOMPATIBLE_REGISTRY_SCOPED_PROPERTIES: Set<string> = new Set([
  */
 const PROPERTY_NAME_REGEX: RegExp = /^([^=\[\s]+)/;
 
+/**
+ * Regular expression to extract environment variable names and optional fallback values.
+ * Matches patterns like:
+ *   nameString                 -> group 1: nameString,    group 2: undefined
+ *   nameString-fallbackString  -> group 1: nameString,    group 2: fallbackString
+ *   nameString:-fallbackString -> group 1: nameString,    group 2: fallbackString
+ */
+const ENV_VAR_WITH_FALLBACK_REGEX: RegExp = /^(?<name>[^:-]+)(?::?-(?<fallback>.+))?$/;
+
 /**
  *
  * @param npmrcFileLines The npmrc file's lines
@@ -188,7 +199,7 @@ export function trimNpmrcFileLines(
              * ${nameString-fallbackString}   -> name-fallbackString
              * ${nameString:-fallbackString}  -> name:-fallbackString
              */
-            const nameWithFallback: string = token.substring(2, token.length - 1);
+            const nameWithFallback: string = token.slice(2, -1);
 
             let environmentVariableName: string;
             let fallback: string | undefined;
@@ -201,10 +212,9 @@ export function trimNpmrcFileLines(
                * nameString-fallbackString  ->  nameString    fallbackString
                * nameString:-fallbackString ->  nameString    fallbackString
                */
-              const matched: string[] | null = nameWithFallback.match(/^([^:-]+)(?:\:?-(.+))?$/);
-              // matched: [originStr, variableName, fallback]
-              environmentVariableName = matched?.[1] ?? nameWithFallback;
-              fallback = matched?.[2];
+              const matched: RegExpMatchArray | null = nameWithFallback.match(ENV_VAR_WITH_FALLBACK_REGEX);
+              environmentVariableName = matched?.groups?.name ?? nameWithFallback;
+              fallback = matched?.groups?.fallback;
             } else {
               environmentVariableName = nameWithFallback;
             }
@@ -262,6 +272,7 @@ interface INpmrcTrimOptions {
   linesToAppend?: string[];
   supportEnvVarFallbackSyntax: boolean;
   filterNpmIncompatibleProperties?: boolean;
+  env?: NodeJS.ProcessEnv;
 }
 
 function _copyAndTrimNpmrcFile(options: INpmrcTrimOptions): string {
@@ -295,6 +306,7 @@ export interface ISyncNpmrcOptions {
   linesToAppend?: string[];
   createIfMissing?: boolean;
   filterNpmIncompatibleProperties?: boolean;
+  env?: NodeJS.ProcessEnv;
 }
 
 export function syncNpmrc(options: ISyncNpmrcOptions): string | undefined {