diff --git a/.gitignore b/.gitignore
index d536d0bb5ea..1f7c828e001 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,7 +3,7 @@ config.local.json
 /node_modules/
 local.log
 /patches/
-/dist
+**/dist
 tmp
 .DS_Store
 /package-lock.json
@@ -24,3 +24,4 @@ report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
 /test/acceptance/workspaces/**/project/
 /test/acceptance/workspaces/**/target/
 test/acceptance/workspaces/**/.gradle
+test/**/.gradle
diff --git a/package.json b/package.json
index d1833088e17..7b66d786651 100644
--- a/package.json
+++ b/package.json
@@ -53,7 +53,7 @@
   "author": "snyk.io",
   "license": "Apache-2.0",
   "dependencies": {
-    "@snyk/cli-interface": "2.8.1",
+    "@snyk/cli-interface": "2.9.0",
     "@snyk/dep-graph": "1.19.3",
     "@snyk/gemfile": "1.2.0",
     "@snyk/graphlib": "2.1.9-patch",
diff --git a/src/lib/find-files.ts b/src/lib/find-files.ts
index c89eb3b64a7..bc9708141dc 100644
--- a/src/lib/find-files.ts
+++ b/src/lib/find-files.ts
@@ -39,6 +39,11 @@ export async function getStats(path: string): Promise<fs.Stats> {
   });
 }
 
+interface FindFilesRes {
+  files: string[];
+  allFilesFound: string[];
+}
+
 /**
  * Find all files in given search path. Returns paths to files found.
  *
@@ -52,11 +57,13 @@ export async function find(
   ignore: string[] = [],
   filter: string[] = [],
   levelsDeep = 4,
-): Promise<string[]> {
+): Promise<FindFilesRes> {
   const found: string[] = [];
+  const foundAll: string[] = [];
+
   // ensure we ignore find against node_modules path.
   if (path.endsWith('node_modules')) {
-    return found;
+    return { files: found, allFilesFound: foundAll };
   }
   // ensure node_modules is always ignored
   if (!ignore.includes('node_modules')) {
@@ -64,22 +71,36 @@ export async function find(
   }
   try {
     if (levelsDeep < 0) {
-      return found;
+      return { files: found, allFilesFound: foundAll };
     } else {
       levelsDeep--;
     }
     const fileStats = await getStats(path);
     if (fileStats.isDirectory()) {
-      const files = await findInDirectory(path, ignore, filter, levelsDeep);
+      const { files, allFilesFound } = await findInDirectory(
+        path,
+        ignore,
+        filter,
+        levelsDeep,
+      );
       found.push(...files);
+      foundAll.push(...allFilesFound);
     } else if (fileStats.isFile()) {
       const fileFound = findFile(path, filter);
       if (fileFound) {
         found.push(fileFound);
+        foundAll.push(fileFound);
       }
     }
-
-    return filterForDefaultManifests(found);
+    const filteredOutFiles = foundAll.filter((f) => !found.includes(f));
+    if (filteredOutFiles.length) {
+      debug(
+        `Filtered out ${filteredOutFiles.length}/${
+          foundAll.length
+        } files: ${foundAll.join(', ')}`,
+      );
+    }
+    return { files: filterForDefaultManifests(found), allFilesFound: foundAll };
   } catch (err) {
     throw new Error(`Error finding files in path '${path}'.\n${err.message}`);
   }
@@ -102,7 +123,7 @@ async function findInDirectory(
   ignore: string[] = [],
   filter: string[] = [],
   levelsDeep = 4,
-): Promise<string[]> {
+): Promise<FindFilesRes> {
   const files = await readDirectory(path);
   const toFind = files
     .filter((file) => !ignore.includes(file))
@@ -110,12 +131,22 @@ async function findInDirectory(
       const resolvedPath = pathLib.resolve(path, file);
       if (!fs.existsSync(resolvedPath)) {
         debug('File does not seem to exist, skipping: ', file);
-        return [];
+        return { files: [], allFilesFound: [] };
       }
       return find(resolvedPath, ignore, filter, levelsDeep);
     });
+
   const found = await Promise.all(toFind);
-  return Array.prototype.concat.apply([], found);
+  return {
+    files: Array.prototype.concat.apply(
+      [],
+      found.map((f) => f.files),
+    ),
+    allFilesFound: Array.prototype.concat.apply(
+      [],
+      found.map((f) => f.allFilesFound),
+    ),
+  };
 }
 
 function filterForDefaultManifests(files: string[]): string[] {
diff --git a/src/lib/plugins/get-deps-from-plugin.ts b/src/lib/plugins/get-deps-from-plugin.ts
index 4fd4117e65f..79e91696e06 100644
--- a/src/lib/plugins/get-deps-from-plugin.ts
+++ b/src/lib/plugins/get-deps-from-plugin.ts
@@ -1,4 +1,6 @@
 import * as debugModule from 'debug';
+import * as pathLib from 'path';
+import chalk from 'chalk';
 import { legacyPlugin as pluginApi } from '@snyk/cli-interface';
 import { find } from '../find-files';
 import { Options, TestOptions, MonitorOptions } from '../types';
@@ -17,6 +19,7 @@ import analytics = require('../analytics');
 import { convertSingleResultToMultiCustom } from './convert-single-splugin-res-to-multi-custom';
 import { convertMultiResultToMultiCustom } from './convert-multi-plugin-res-to-multi-custom';
 import { processYarnWorkspaces } from './nodejs-plugin/yarn-workspaces-parser';
+import { ScannedProject } from '@snyk/cli-interface/legacy/common';
 
 const debug = debugModule('snyk-test');
 
@@ -42,7 +45,7 @@ export async function getDepsFromPlugin(
     const scanType = options.yarnWorkspaces ? 'yarnWorkspaces' : 'allProjects';
     const levelsDeep = options.detectionDepth;
     const ignore = options.exclude ? options.exclude.split(',') : [];
-    const targetFiles = await find(
+    const { files: targetFiles, allFilesFound } = await find(
       root,
       ignore,
       multiProjectProcessors[scanType].files,
@@ -62,8 +65,9 @@ export async function getDepsFromPlugin(
       options,
       targetFiles,
     );
+    const scannedProjects = inspectRes.scannedProjects;
     const analyticData = {
-      scannedProjects: inspectRes.scannedProjects.length,
+      scannedProjects: scannedProjects.length,
       targetFiles,
       packageManagers: targetFiles.map((file) =>
         detectPackageManagerFromFile(file),
@@ -72,6 +76,18 @@ export async function getDepsFromPlugin(
       ignore,
     };
     analytics.add(scanType, analyticData);
+    debug(
+      `Found ${scannedProjects.length} projects from ${allFilesFound.length} detected manifests`,
+    );
+    const userWarningMessage = warnSomeGradleManifestsNotScanned(
+      scannedProjects,
+      allFilesFound,
+      root,
+    );
+
+    if (!options.json && userWarningMessage) {
+      console.warn(chalk.bold.red(userWarningMessage));
+    }
     return inspectRes;
   }
 
@@ -105,3 +121,35 @@ export async function getDepsFromPlugin(
   );
   return convertMultiResultToMultiCustom(inspectRes, options.packageManager);
 }
+
+export function warnSomeGradleManifestsNotScanned(
+  scannedProjects: ScannedProject[],
+  allFilesFound: string[],
+  root: string,
+): string | null {
+  const gradleTargetFilesFilter = (targetFile) =>
+    targetFile &&
+    (targetFile.endsWith('build.gradle') ||
+      targetFile.endsWith('build.gradle.kts'));
+  const scannedGradleFiles = scannedProjects
+    .map((p) => {
+      const targetFile = p.meta?.targetFile || p.targetFile;
+      return targetFile ? pathLib.resolve(root, targetFile) : null;
+    })
+    .filter(gradleTargetFilesFilter);
+  const detectedGradleFiles = allFilesFound.filter(gradleTargetFilesFilter);
+  const diff = detectedGradleFiles.filter(
+    (file) => !scannedGradleFiles.includes(file),
+  );
+
+  debug(
+    `These Gradle manifests did not return any dependency results:\n${diff.join(
+      ',\n',
+    )}`,
+  );
+
+  if (diff.length > 0) {
+    return `✗ ${diff.length}/${detectedGradleFiles.length} detected Gradle manifests did not return dependencies.\nThey may have errored or were not included as part of a multi-project build. You may need to scan them individually with --file=path/to/file. Run with \`-d\` for more info.`;
+  }
+  return null;
+}
diff --git a/src/lib/plugins/get-extra-project-count.ts b/src/lib/plugins/get-extra-project-count.ts
index 8c40a71d7d0..8d31f99a6c7 100644
--- a/src/lib/plugins/get-extra-project-count.ts
+++ b/src/lib/plugins/get-extra-project-count.ts
@@ -19,7 +19,11 @@ export async function getExtraProjectCount(
     return inspectResult.plugin.meta.allSubProjectNames.length;
   }
   try {
-    const extraTargetFiles = await find(root, [], AUTO_DETECTABLE_FILES);
+    const { files: extraTargetFiles } = await find(
+      root,
+      [],
+      AUTO_DETECTABLE_FILES,
+    );
     const foundProjectsCount =
       extraTargetFiles.length > 1 ? extraTargetFiles.length - 1 : undefined;
     return foundProjectsCount;
diff --git a/src/lib/plugins/nodejs-plugin/npm-lock-parser.ts b/src/lib/plugins/nodejs-plugin/npm-lock-parser.ts
index 0d2a9f13f33..71e864ec77b 100644
--- a/src/lib/plugins/nodejs-plugin/npm-lock-parser.ts
+++ b/src/lib/plugins/nodejs-plugin/npm-lock-parser.ts
@@ -58,6 +58,6 @@ export async function parse(
       strictOutOfSync,
     );
   } finally {
-    await spinner.clear(resolveModuleSpinnerLabel);
+    await spinner.clear<void>(resolveModuleSpinnerLabel)();
   }
 }
diff --git a/test/acceptance/cli-test/cli-test.all-projects.spec.ts b/test/acceptance/cli-test/cli-test.all-projects.spec.ts
index 90862be8034..2e9a07a69f0 100644
--- a/test/acceptance/cli-test/cli-test.all-projects.spec.ts
+++ b/test/acceptance/cli-test/cli-test.all-projects.spec.ts
@@ -4,40 +4,112 @@ import * as depGraphLib from '@snyk/dep-graph';
 import { CommandResult } from '../../../src/cli/commands/types';
 import { AcceptanceTests } from './cli-test.acceptance.test';
 import { getWorkspaceJSON } from '../workspace-helper';
+import * as getDepsFromPlugin from '../../../src/lib/plugins/get-deps-from-plugin';
+
+const simpleGradleGraph = depGraphLib.createFromJSON({
+  schemaVersion: '1.2.0',
+  pkgManager: {
+    name: 'gradle',
+  },
+  pkgs: [
+    {
+      id: 'gradle-monorepo@0.0.0',
+      info: {
+        name: 'gradle-monorepo',
+        version: '0.0.0',
+      },
+    },
+  ],
+  graph: {
+    rootNodeId: 'root-node',
+    nodes: [
+      {
+        nodeId: 'root-node',
+        pkgId: 'gradle-monorepo@0.0.0',
+        deps: [],
+      },
+    ],
+  },
+});
 
 export const AllProjectsTests: AcceptanceTests = {
   language: 'Mixed',
   tests: {
-    '`test kotlin-monorepo --all-projects` scans kotlin files': (
+    '`test gradle-with-orphaned-build-file --all-projects` warns user': (
       params,
       utils,
     ) => async (t) => {
       utils.chdirWorkspaces();
-      const simpleGradleGraph = depGraphLib.createFromJSON({
-        schemaVersion: '1.2.0',
-        pkgManager: {
-          name: 'gradle',
-        },
-        pkgs: [
-          {
-            id: 'gradle-monorepo@0.0.0',
-            info: {
-              name: 'gradle-monorepo',
-              version: '0.0.0',
-            },
-          },
-        ],
-        graph: {
-          rootNodeId: 'root-node',
-          nodes: [
-            {
-              nodeId: 'root-node',
-              pkgId: 'gradle-monorepo@0.0.0',
-              deps: [],
+      const plugin = {
+        async inspect() {
+          return {
+            plugin: {
+              name: 'bundled:gradle',
+              runtime: 'unknown',
+              meta: {},
             },
-          ],
+            scannedProjects: [
+              {
+                meta: {
+                  gradleProjectName: 'root-proj',
+                  versionBuildInfo: {
+                    gradleVersion: '6.5',
+                  },
+                  targetFile: 'build.gradle',
+                },
+                depGraph: simpleGradleGraph,
+              },
+              {
+                meta: {
+                  gradleProjectName: 'root-proj/subproj',
+                  versionBuildInfo: {
+                    gradleVersion: '6.5',
+                  },
+                  targetFile: 'subproj/build.gradle',
+                },
+                depGraph: simpleGradleGraph,
+              },
+            ],
+          };
         },
-      });
+      };
+      const loadPlugin = sinon.stub(params.plugins, 'loadPlugin');
+      t.teardown(loadPlugin.restore);
+      loadPlugin.withArgs('gradle').returns(plugin);
+      loadPlugin.callThrough();
+      // read data from console.log
+      let stdoutMessages = '';
+      const stubConsoleLog = (msg: string) => (stdoutMessages += msg);
+      const stubbedConsole = sinon
+        .stub(console, 'warn')
+        .callsFake(stubConsoleLog);
+      const result: CommandResult = await params.cli.test(
+        'gradle-with-orphaned-build-file',
+        {
+          allProjects: true,
+          detectionDepth: 3,
+        },
+      );
+      t.same(
+        stdoutMessages,
+        '✗ 1/3 detected Gradle manifests did not return dependencies.\n' +
+          'They may have errored or were not included as part of a multi-project build. You may need to scan them individually with --file=path/to/file. Run with `-d` for more info.',
+      );
+      stubbedConsole.restore();
+      t.ok(stubbedConsole.calledOnce);
+      t.ok(loadPlugin.withArgs('gradle').calledOnce, 'calls gradle plugin');
+
+      t.match(
+        result.getDisplayResults(),
+        'Tested 2 projects',
+        'Detected 2 projects',
+      );
+    },
+    '`test kotlin-monorepo --all-projects` scans kotlin files': (
+      params,
+      utils,
+    ) => async (t) => {
+      utils.chdirWorkspaces();
       const plugin = {
         async inspect() {
           return {
diff --git a/test/acceptance/workspaces/gradle-with-orphaned-build-file/build.gradle b/test/acceptance/workspaces/gradle-with-orphaned-build-file/build.gradle
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/acceptance/workspaces/gradle-with-orphaned-build-file/orphaned/build.gradle b/test/acceptance/workspaces/gradle-with-orphaned-build-file/orphaned/build.gradle
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/acceptance/workspaces/gradle-with-orphaned-build-file/settings.gradle b/test/acceptance/workspaces/gradle-with-orphaned-build-file/settings.gradle
new file mode 100644
index 00000000000..90289e8a32b
--- /dev/null
+++ b/test/acceptance/workspaces/gradle-with-orphaned-build-file/settings.gradle
@@ -0,0 +1,5 @@
+rootProject.name = 'root-proj'
+
+include 'subproj'
+
+
diff --git a/test/acceptance/workspaces/gradle-with-orphaned-build-file/subproj/build.gradle b/test/acceptance/workspaces/gradle-with-orphaned-build-file/subproj/build.gradle
new file mode 100644
index 00000000000..301e7be03bc
--- /dev/null
+++ b/test/acceptance/workspaces/gradle-with-orphaned-build-file/subproj/build.gradle
@@ -0,0 +1,51 @@
+apply plugin: 'java'
+apply plugin: 'maven'
+
+group = 'com.github.jitpack'
+
+sourceCompatibility = 1.8 // java 8
+targetCompatibility = 1.8
+
+repositories {
+  mavenCentral()
+}
+
+dependencies {
+  // Gradle 3+ will not pick up "compile" dependencies for "compileOnly"
+  // Gradle 2 will, so for configuration-matching tests we use "runtime"
+  runtime 'com.google.guava:guava:18.0'
+  runtime 'batik:batik-dom:1.6'
+  runtime 'commons-discovery:commons-discovery:0.2'
+  compileOnly 'axis:axis:1.3'
+  runtime 'com.android.tools.build:builder:2.3.0'
+}
+
+task sourcesJar(type: Jar, dependsOn: classes) {
+    classifier = 'sources'
+    from sourceSets.main.allSource
+}
+
+task javadocJar(type: Jar, dependsOn: javadoc) {
+    classifier = 'javadoc'
+    from javadoc.destinationDir
+}
+
+artifacts {
+    archives sourcesJar
+    archives javadocJar
+}
+
+// To specify a license in the pom:
+install {
+  repositories.mavenInstaller {
+    pom.project {
+      licenses {
+        license {
+          name 'The Apache Software License, Version 2.0'
+          url 'http://www.apache.org/licenses/LICENSE-2.0.txt'
+          distribution 'repo'
+        }
+      }
+    }
+  }
+}
diff --git a/test/find-files.test.ts b/test/find-files.test.ts
index aa34873061c..d37558f26e9 100644
--- a/test/find-files.test.ts
+++ b/test/find-files.test.ts
@@ -6,7 +6,7 @@ const testFixture = path.join(__dirname, 'fixtures', 'find-files');
 
 test('find all files in test fixture', async (t) => {
   // six levels deep to find all
-  const result = await find(testFixture, [], [], 6);
+  const { files: result, allFilesFound } = await find(testFixture, [], [], 6);
   const expected = [
     path.join(
       testFixture,
@@ -29,13 +29,46 @@ test('find all files in test fixture', async (t) => {
     path.join(testFixture, 'ruby', 'Gemfile.lock'),
     path.join(testFixture, 'yarn', 'yarn.lock'),
   ];
+  const filteredOut = [
+    path.join(testFixture, 'golang', 'golang-app', 'Gopkg.toml'),
+    path.join(testFixture, 'README.md'),
+    path.join(testFixture, 'yarn', 'package.json'),
+    path.join(testFixture, 'ruby', 'Gemfile'),
+    path.join(testFixture, 'gradle-kts', 'subproj', 'build.gradle.kts'),
+    path.join(testFixture, 'npm-with-lockfile', 'package.json'),
+    path.join(testFixture, 'gradle', 'subproject', 'build.gradle'),
+    path.join(testFixture, 'gradle-and-kotlin', 'build.gradle.kts'),
+    path.join(
+      testFixture,
+      'gradle-multiple',
+      'gradle',
+      'subproject',
+      'build.gradle',
+    ),
+    path.join(
+      testFixture,
+      'gradle-multiple',
+      'gradle-another',
+      'subproject',
+      'build.gradle',
+    ),
+    path.join(testFixture, 'maven', 'test.txt'),
+    path.join(testFixture, 'mvn', 'test.txt'),
+    path.join(testFixture, 'npm', 'test.txt'),
+    path.join(testFixture, 'ruby', 'test.txt'),
+  ];
   t.same(result.length, expected.length, 'should be the same length');
   t.same(result.sort(), expected.sort(), 'should return all files');
+  t.same(
+    allFilesFound.filter((f) => !f.endsWith('broken-symlink')).sort(),
+    [...filteredOut, ...expected].sort(),
+    'should return all unfiltered files',
+  );
 });
 
 test('find all files in test fixture ignoring node_modules', async (t) => {
   // six levels deep to ensure node_modules is tested
-  const result = await find(testFixture, ['node_modules'], [], 6);
+  const { files: result } = await find(testFixture, ['node_modules'], [], 6);
   const expected = [
     path.join(
       testFixture,
@@ -64,14 +97,19 @@ test('find all files in test fixture ignoring node_modules', async (t) => {
 test('find package.json file in test fixture ignoring node_modules', async (t) => {
   // six levels deep to ensure node_modules is tested
   const nodeModulesPath = path.join(testFixture, 'node_modules');
-  const result = await find(nodeModulesPath, [], ['package.json'], 6);
+  const { files: result } = await find(
+    nodeModulesPath,
+    [],
+    ['package.json'],
+    6,
+  );
   const expected = [];
   t.same(result.sort(), expected.sort(), 'should return expected file');
 });
 
 test('find package.json file in test fixture (by default ignoring node_modules)', async (t) => {
   // six levels deep to ensure node_modules is tested
-  const result = await find(testFixture, [], ['package.json'], 6);
+  const { files: result } = await find(testFixture, [], ['package.json'], 6);
   const expected = [
     path.join(testFixture, 'npm', 'package.json'),
     path.join(testFixture, 'npm-with-lockfile', 'package.json'),
@@ -83,7 +121,7 @@ test('find package.json file in test fixture (by default ignoring node_modules)'
 test('find package-lock.json file in test fixture (ignore package.json in the same folder)', async (t) => {
   const npmLockfilePath = path.join(testFixture, 'npm-with-lockfile');
 
-  const result = await find(
+  const { files: result } = await find(
     npmLockfilePath,
     [],
     ['package.json', 'package-lock.json'],
@@ -96,7 +134,7 @@ test('find package-lock.json file in test fixture (ignore package.json in the sa
 test('find build.gradle file in test fixture (ignore build.gradle in the same folder)', async (t) => {
   const buildGradle = path.join(testFixture, 'gradle-and-kotlin');
 
-  const result = await find(
+  const { files: result } = await find(
     buildGradle,
     [],
     ['build.gradle.kts', 'build.gradle'],
@@ -109,7 +147,7 @@ test('find build.gradle file in test fixture (ignore build.gradle in the same fo
 test('find Gemfile.lock file in test fixture (ignore Gemfile in the same folder)', async (t) => {
   const npmLockfilePath = path.join(testFixture, 'ruby');
 
-  const result = await find(
+  const { files: result } = await find(
     npmLockfilePath,
     [],
     ['Gemfile', 'Gemfile.lock'],
@@ -122,7 +160,7 @@ test('find Gemfile.lock file in test fixture (ignore Gemfile in the same folder)
 test('find yarn.lock file in test fixture (ignore package.json in the same folder)', async (t) => {
   const yarnLockfilePath = path.join(testFixture, 'yarn');
 
-  const result = await find(
+  const { files: result } = await find(
     yarnLockfilePath,
     [],
     ['package.json', 'yarn.lock'],
@@ -134,7 +172,7 @@ test('find yarn.lock file in test fixture (ignore package.json in the same folde
 
 test('find package.json file in test fixture (by default ignoring node_modules)', async (t) => {
   // four levels deep to ensure node_modules is tested
-  const result = await find(testFixture, [], ['package.json'], 4);
+  const { files: result } = await find(testFixture, [], ['package.json'], 4);
   const expected = [
     path.join(testFixture, 'npm', 'package.json'),
     path.join(testFixture, 'npm-with-lockfile', 'package.json'),
@@ -144,13 +182,13 @@ test('find package.json file in test fixture (by default ignoring node_modules)'
 });
 
 test('find Gemfile file in test fixture', async (t) => {
-  const result = await find(testFixture, [], ['Gemfile']);
+  const { files: result } = await find(testFixture, [], ['Gemfile']);
   const expected = [path.join(testFixture, 'ruby', 'Gemfile')];
   t.same(result.sort(), expected.sort(), 'should return expected file');
 });
 
 test('find pom.xml files in test fixture', async (t) => {
-  const result = await find(testFixture, [], ['pom.xml']);
+  const { files: result } = await find(testFixture, [], ['pom.xml']);
   const expected = [
     path.join(testFixture, 'maven', 'pom.xml'),
     path.join(testFixture, 'mvn', 'pom.xml'),