diff --git a/src/client/metadataApiDeploy.ts b/src/client/metadataApiDeploy.ts
index 8945d4157..60cbb19fd 100644
--- a/src/client/metadataApiDeploy.ts
+++ b/src/client/metadataApiDeploy.ts
@@ -68,12 +68,15 @@ export class DeployResult implements MetadataTransferResult {
     // this involves FS operations, so only perform once!
     if (!this.fileResponses) {
       this.fileResponses = [
-        // removes duplicates from the file responses by parsing the object into a string, used as the key of the map
         ...new Map(
           (this.components
             ? buildFileResponsesFromComponentSet(this.components)(this.response)
             : buildFileResponses(this.response)
-          ).map((v) => [JSON.stringify(v), v])
+          ).map((v) => {
+            const base = `${v.type}#${v.fullName}#${v.filePath ?? ''}#${v.state}`;
+            const key = 'error' in v ? `${base}#${v.error}#${String(v.lineNumber)}#${String(v.columnNumber)}` : base;
+            return [key, v] as const;
+          })
         ).values(),
       ];
     }
@@ -465,24 +468,26 @@ const deleteNotFoundToFileResponses =
           : [];
       });
 
+const MANIFEST_FILES = new Set([
+  'package.xml',
+  'destructiveChanges.xml',
+  'destructiveChangesPost.xml',
+  'destructiveChangesPre.xml',
+]);
+
 const warnIfUnmatchedServerResult =
   (fr: FileResponse[]) =>
-  (messageMap: Map<string, DeployMessage[]>): void[] =>
-    // keep the parents and children separated for MPD scenarios where we have a parent in one, children in another package
-    [...messageMap.keys()].flatMap((key) => {
+  (messageMap: Map<string, DeployMessage[]>): void[] => {
+    const frKeys = new Set(fr.map((c) => `${c.type}#${c.fullName}`));
+
+    return [...messageMap.keys()].flatMap((key) => {
       const [type, fullName] = key.split('#', 2);
 
       // UIBundleResource messages are already handled by the parent UIBundle component
       const consumedByWebApp =
         type === 'UIBundleResource' && fr.some((c) => c.type === 'UIBundle' && fullName.startsWith(`${c.fullName}/`));
 
-      if (
-        !consumedByWebApp &&
-        !fr.find((c) => c.type === type && c.fullName === fullName) &&
-        !['package.xml', 'destructiveChanges.xml', 'destructiveChangesPost.xml', 'destructiveChangesPre.xml'].includes(
-          fullName
-        )
-      ) {
+      if (!consumedByWebApp && !frKeys.has(key) && !MANIFEST_FILES.has(fullName)) {
         const deployMessage = messageMap.get(key)!.at(0)!;
 
         // Don't warn for deleted components - not found in the component set (pre-destructiveChanges)
@@ -498,6 +503,7 @@ const warnIfUnmatchedServerResult =
         );
       }
     });
+  };
 const buildFileResponses = (response: MetadataApiDeployStatus): FileResponse[] =>
   ensureArray(response.details?.componentSuccesses)
     .concat(ensureArray(response.details?.componentFailures))
@@ -525,7 +531,7 @@ const buildFileResponsesFromComponentSet =
   (response: MetadataApiDeployStatus): FileResponse[] => {
     const responseMessages = getDeployMessages(response);
 
-    const fileResponses: FileResponse[] = (cs.getSourceComponents().toArray() ?? [])
+    const fileResponses: FileResponse[] = [...cs.getSourceComponents()]
       .flatMap((deployedComponent): FileResponse[] => {
         // UIBundle bundles get per-file status via UIBundleResource messages
         if (
diff --git a/src/collections/componentSet.ts b/src/collections/componentSet.ts
index 3566dd9a2..091c93815 100644
--- a/src/collections/componentSet.ts
+++ b/src/collections/componentSet.ts
@@ -522,7 +522,7 @@ export class ComponentSet extends LazyCollection<MetadataComponent> {
     });
     const toParse = await this.getObject(destructiveType);
     toParse.Package[XML_NS_KEY] = XML_NS_URL;
-     
+
     return XML_DECL.concat(builder.build(toParse));
   }
 
diff --git a/src/resolve/adapters/baseSourceAdapter.ts b/src/resolve/adapters/baseSourceAdapter.ts
index 65ed3ceee..c4f188181 100644
--- a/src/resolve/adapters/baseSourceAdapter.ts
+++ b/src/resolve/adapters/baseSourceAdapter.ts
@@ -29,6 +29,9 @@ import { RegistryAccess } from '../../registry/registryAccess';
 Messages.importMessagesDirectory(__dirname);
 const messages = Messages.loadMessages('@salesforce/source-deploy-retrieve', 'sdr');
 
+const NAME_AND_SUFFIX_REGEX = /(.+)\.(.+)/;
+const FOLDER_META_XML_STRICT_REGEX = /(.+)-meta\.xml$/;
+
 export abstract class BaseSourceAdapter implements SourceAdapter {
   protected type: MetadataType;
   protected registry: RegistryAccess;
@@ -191,14 +194,14 @@ const parseAsContentMetadataXml =
       return undefined;
     }
 
-    const match = new RegExp(/(.+)\.(.+)/).exec(basename(path));
+    const match = NAME_AND_SUFFIX_REGEX.exec(basename(path));
     if (match && type.suffix === match[2]) {
       return { fullName: match[1], suffix: match[2], path };
     }
   };
 
 const parseAsFolderMetadataXml = (fsPath: SourcePath): MetadataXml | undefined => {
-  const match = new RegExp(/(.+)-meta\.xml$/).exec(basename(fsPath));
+  const match = FOLDER_META_XML_STRICT_REGEX.exec(basename(fsPath));
   const parts = fsPath.split(sep);
   if (match && !match[1].includes('.') && parts.length > 1) {
     return { fullName: match[1], suffix: undefined, path: fsPath };
diff --git a/src/resolve/metadataResolver.ts b/src/resolve/metadataResolver.ts
index 84d09accf..c6b2b7e46 100644
--- a/src/resolve/metadataResolver.ts
+++ b/src/resolve/metadataResolver.ts
@@ -31,6 +31,9 @@ import { NodeFSTreeContainer, TreeContainer } from './treeContainers';
 Messages.importMessagesDirectory(__dirname);
 const messages = Messages.loadMessages('@salesforce/source-deploy-retrieve', 'sdr');
 
+const CLOSE_META_SUFFIX_REGEX = /.+\.([^.-]+)(?:-.*)?\.xml/;
+const FOLDER_META_XML_REGEX = /(.+)-meta\.xml/;
+
 /**
  * Resolver for metadata type and component objects.
  *
@@ -262,7 +265,7 @@ const getSuggestionsForUnresolvedTypes =
     const metaSuffix = parsedMetaXml?.suffix;
     // Finds close matches for meta suffixes
     // Examples: https://regex101.com/r/vbRjwy/1
-    const closeMetaSuffix = new RegExp(/.+\.([^.-]+)(?:-.*)?\.xml/).exec(basename(fsPath));
+    const closeMetaSuffix = CLOSE_META_SUFFIX_REGEX.exec(basename(fsPath));
 
     let guesses;
 
@@ -307,7 +310,7 @@ const parseAsFolderMetadataXml =
   (registry: RegistryAccess) =>
   (fsPath: string): string | undefined => {
     let folderName: string | undefined;
-    const match = new RegExp(/(.+)-meta\.xml/).exec(basename(fsPath));
+    const match = FOLDER_META_XML_REGEX.exec(basename(fsPath));
     if (match && !match[1].includes('.')) {
       const parts = fsPath.split(sep);
       if (parts.length > 1) {
diff --git a/src/resolve/treeContainers.ts b/src/resolve/treeContainers.ts
index e0a8e6fba..a3c5371b4 100644
--- a/src/resolve/treeContainers.ts
+++ b/src/resolve/treeContainers.ts
@@ -124,9 +124,13 @@ export class NodeFSTreeContainer extends TreeContainer {
   }
 
   public readDirectory(fsPath: SourcePath): string[] {
-    const resolved = this.getUpdatedFsPath(fsPath);
-    if (!statSync(resolved).isDirectory()) return [];
-    return readdirSync(resolved);
+    try {
+      return readdirSync(this.getUpdatedFsPath(fsPath));
+    } catch (e) {
+      const code = (e as NodeJS.ErrnoException).code;
+      if (code === 'ENOTDIR' || code === 'ENOENT') return [];
+      throw e;
+    }
   }
 
   public readFile(fsPath: SourcePath): Promise<Buffer> {
@@ -152,15 +156,33 @@ export class NodeFSTreeContainer extends TreeContainer {
 export class ZipTreeContainer extends TreeContainer {
   private zip: JSZip;
   private zipKeyMap: Map<string, string> = new Map<string, string>();
+  private dirChildren: Map<string, string[]> = new Map<string, string[]>();
 
   private constructor(zip: JSZip) {
     super();
     this.zip = zip;
     for (const key of Object.keys(this.zip.files)) {
       if (key.endsWith('/')) {
-        this.zipKeyMap.set(key.slice(0, -1), key);
+        const normalized = key.slice(0, -1);
+        this.zipKeyMap.set(normalized, key);
+        const dir = dirname(normalized);
+        if (dir !== normalized) {
+          let children = this.dirChildren.get(dir);
+          if (!children) {
+            children = [];
+            this.dirChildren.set(dir, children);
+          }
+          children.push(basename(normalized));
+        }
       } else {
         this.zipKeyMap.set(key, key);
+        const dir = dirname(key);
+        let children = this.dirChildren.get(dir);
+        if (!children) {
+          children = [];
+          this.dirChildren.set(dir, children);
+        }
+        children.push(basename(key));
       }
     }
   }
@@ -185,12 +207,8 @@ export class ZipTreeContainer extends TreeContainer {
   public readDirectory(fsPath: string): string[] {
     const resolvedPath = this.match(fsPath);
     if (resolvedPath && this.ensureDirectory(resolvedPath)) {
-      // Remove trailing path sep if it exists. JSZip always adds them for directories but
-      // when comparing we call `dirname()` which does not include them.
       const dirPath = resolvedPath.endsWith('/') ? resolvedPath.slice(0, -1) : resolvedPath;
-      return Object.keys(this.zip.files)
-        .filter((filePath) => dirname(filePath) === dirPath)
-        .map((filePath) => basename(filePath));
+      return this.dirChildren.get(dirPath) ?? [];
     }
     throw new SfError(messages.getMessage('error_expected_directory_path', [fsPath]), 'LibraryError');
   }
diff --git a/src/utils/path.ts b/src/utils/path.ts
index e79c2808f..d5fee2917 100644
--- a/src/utils/path.ts
+++ b/src/utils/path.ts
@@ -96,8 +96,10 @@ export function trimUntil(fsPath: SourcePath, part: string, untilLast = false):
  * @param fsPath - File path to parse
  * @returns MetadataXml info or undefined
  */
+const METADATA_XML_REGEX = /(.+)\.(.+)-meta\.xml/;
+
 export function parseMetadataXml(fsPath: string): Optional<MetadataXml> {
-  const match = new RegExp(/(.+)\.(.+)-meta\.xml/).exec(basename(fsPath));
+  const match = METADATA_XML_REGEX.exec(basename(fsPath));
   if (match) {
     return { fullName: match[1], suffix: match[2], path: fsPath };
   }