diff --git a/packages/providence-analytics/test-node/cli/cli.test.js b/packages/providence-analytics/test-node/cli/cli.test.js
index 7fb19d554..1b5c79caa 100644
--- a/packages/providence-analytics/test-node/cli/cli.test.js
+++ b/packages/providence-analytics/test-node/cli/cli.test.js
@@ -13,147 +13,334 @@ const {
   suppressNonCriticalLogs,
   restoreSuppressNonCriticalLogs,
 } = require('../../test-helpers/mock-log-service-helpers.js');
-
+const { InputDataService } = require('../../src/program/services/InputDataService.js');
 const { QueryService } = require('../../src/program/services/QueryService.js');
-
 const providenceModule = require('../../src/program/providence.js');
 const extendDocsModule = require('../../src/cli/generate-extend-docs-data.js');
-
-const dummyAnalyzer = require('../../test-helpers/templates/analyzer-template.js');
+const cliHelpersModule = require('../../src/cli/cli-helpers.js');
 const { cli } = require('../../src/cli/cli.js');
-const { pathsArrayFromCs } = require('../../src/cli/cli-helpers.js');
+const promptAnalyzerModule = require('../../src/cli/prompt-analyzer-menu.js');
+
+const {
+  pathsArrayFromCs,
+  pathsArrayFromCollectionName,
+  appendProjectDependencyPaths,
+} = cliHelpersModule;
 
 const queryResults = [];
 const rootDir = pathLib.resolve(__dirname, '../../');
 
+const externalCfgMock = {
+  searchTargetCollections: {
+    'lion-collection': [
+      './providence-input-data/search-targets/example-project-a',
+      './providence-input-data/search-targets/example-project-b',
+      // ...etc
+    ],
+  },
+  referenceCollections: {
+    'lion-based-ui-collection': [
+      './providence-input-data/references/lion-based-ui',
+      './providence-input-data/references/lion-based-ui-labs',
+    ],
+  },
+};
+
+async function runCli(args, cwd) {
+  process.argv = [...process.argv.slice(0, 2), ...args.split(' ')];
+  await cli({ cwd });
+}
+
 describe('Providence CLI', () => {
+  let providenceStub;
+  let promptCfgStub;
+  let iExtConfStub;
+  let promptStub;
+  let qConfStub;
+
   before(() => {
-    suppressNonCriticalLogs();
     mockWriteToJson(queryResults);
+    suppressNonCriticalLogs();
 
     mockProject(
       {
         './src/OriginalComp.js': `export class OriginalComp {}`,
         './src/inbetween.js': `export { OriginalComp as InBetweenComp } from './OriginalComp.js'`,
         './index.js': `export { InBetweenComp as MyComp } from './src/inbetween.js'`,
+        './node_modules/dependency-a/index.js': '',
+        './bower_components/dependency-b/index.js': '',
       },
       {
         projectName: 'example-project',
         projectPath: '/mocked/path/example-project',
       },
     );
+
+    providenceStub = sinon.stub(providenceModule, 'providence').returns(
+      new Promise(resolve => {
+        resolve();
+      }),
+    );
+
+    promptCfgStub = sinon
+      .stub(promptAnalyzerModule, 'promptAnalyzerConfigMenu')
+      .returns({ analyzerConfig: { con: 'fig' } });
+
+    iExtConfStub = sinon.stub(InputDataService, 'getExternalConfig').returns(externalCfgMock);
+
+    promptStub = sinon
+      .stub(promptAnalyzerModule, 'promptAnalyzerMenu')
+      .returns({ analyzerName: 'mock-analyzer' });
+
+    qConfStub = sinon.stub(QueryService, 'getQueryConfigFromAnalyzer').returns({
+      analyzer: {
+        name: 'mock-analyzer',
+        requiresReference: true,
+      },
+    });
   });
 
   after(() => {
     restoreSuppressNonCriticalLogs();
-    restoreWriteToJson();
     restoreMockedProjects();
-  });
+    restoreWriteToJson();
 
-  let providenceStub;
-  let qConfStub;
-  beforeEach(() => {
-    qConfStub = sinon.stub(QueryService, 'getQueryConfigFromAnalyzer').returns({ analyzer: {} });
-    providenceStub = sinon.stub(providenceModule, 'providence').returns(Promise.resolve());
-  });
-
-  afterEach(() => {
     providenceStub.restore();
+    promptCfgStub.restore();
+    iExtConfStub.restore();
+    promptStub.restore();
     qConfStub.restore();
   });
 
-  async function runCli(args, cwd) {
-    process.argv = [...process.argv.slice(0, 2), ...args.split(' ')];
-    await cli({ cwd, addProjectDependencyPaths: false });
-  }
-
-  const analyzCmd = 'analyze find-exports';
-
-  it('creates a QueryConfig', async () => {
-    await runCli('analyze find-exports -t /mocked/path/example-project');
-    expect(qConfStub.called).to.be.true;
-    expect(qConfStub.args[0][0]).to.equal('find-exports');
+  afterEach(() => {
+    providenceStub.resetHistory();
+    promptCfgStub.resetHistory();
+    iExtConfStub.resetHistory();
+    promptStub.resetHistory();
+    qConfStub.resetHistory();
   });
 
+  const analyzeCmd = 'analyze mock-analyzer';
+
   it('calls providence', async () => {
-    await runCli(`${analyzCmd} -t /mocked/path/example-project`);
+    await runCli(`${analyzeCmd} -t /mocked/path/example-project`);
     expect(providenceStub.called).to.be.true;
   });
 
+  it('creates a QueryConfig', async () => {
+    await runCli(`${analyzeCmd} -t /mocked/path/example-project`);
+    expect(qConfStub.called).to.be.true;
+    expect(qConfStub.args[0][0]).to.equal('mock-analyzer');
+  });
+
   describe('Global options', () => {
+    let pathsArrayFromCollectionStub;
+    let pathsArrayFromCsStub;
+    let appendProjectDependencyPathsStub;
+
+    before(() => {
+      pathsArrayFromCsStub = sinon
+        .stub(cliHelpersModule, 'pathsArrayFromCs')
+        .returns(['/mocked/path/example-project']);
+      pathsArrayFromCollectionStub = sinon
+        .stub(cliHelpersModule, 'pathsArrayFromCollectionName')
+        .returns(['/mocked/path/example-project']);
+      appendProjectDependencyPathsStub = sinon
+        .stub(cliHelpersModule, 'appendProjectDependencyPaths')
+        .returns([
+          '/mocked/path/example-project',
+          '/mocked/path/example-project/node_modules/mock-dep-a',
+          '/mocked/path/example-project/bower_components/mock-dep-b',
+        ]);
+    });
+
+    after(() => {
+      pathsArrayFromCsStub.restore();
+      pathsArrayFromCollectionStub.restore();
+      appendProjectDependencyPathsStub.restore();
+    });
+
+    afterEach(() => {
+      pathsArrayFromCsStub.resetHistory();
+      pathsArrayFromCollectionStub.resetHistory();
+      appendProjectDependencyPathsStub.resetHistory();
+    });
+
     it('"-e --extensions"', async () => {
-      await runCli(`${analyzCmd} --extensions bla,blu`);
+      await runCli(`${analyzeCmd} -e bla,blu`);
+      expect(providenceStub.args[0][1].gatherFilesConfig.extensions).to.eql(['.bla', '.blu']);
+
+      providenceStub.resetHistory();
+
+      await runCli(`${analyzeCmd} --extensions bla,blu`);
       expect(providenceStub.args[0][1].gatherFilesConfig.extensions).to.eql(['.bla', '.blu']);
     });
 
-    describe('"-t", "--search-target-paths"', async () => {
-      it('allows absolute paths', async () => {
-        await runCli(`${analyzCmd} -t /mocked/path/example-project`, rootDir);
-        expect(providenceStub.args[0][1].targetProjectPaths).to.eql([
-          '/mocked/path/example-project',
-        ]);
-      });
+    it('"-t --search-target-paths"', async () => {
+      await runCli(`${analyzeCmd} -t /mocked/path/example-project`, rootDir);
+      expect(pathsArrayFromCsStub.args[0][0]).to.equal('/mocked/path/example-project');
+      expect(providenceStub.args[0][1].targetProjectPaths).to.eql(['/mocked/path/example-project']);
 
-      it('allows relative paths', async () => {
-        await runCli(
-          `${analyzCmd} -t ./test-helpers/project-mocks/importing-target-project`,
-          rootDir,
-        );
-        expect(providenceStub.args[0][1].targetProjectPaths).to.eql([
-          `${rootDir}/test-helpers/project-mocks/importing-target-project`,
-        ]);
+      pathsArrayFromCsStub.resetHistory();
+      providenceStub.resetHistory();
 
-        await runCli(
-          `${analyzCmd} -t test-helpers/project-mocks/importing-target-project`,
-          rootDir,
-        );
-        expect(providenceStub.args[0][1].targetProjectPaths).to.eql([
-          `${rootDir}/test-helpers/project-mocks/importing-target-project`,
-        ]);
-      });
-
-      // TODO: globbing via cli-helpers doesn't work for some reason when run in this test
-      it.skip('allows globs', async () => {
-        await runCli(`${analyzCmd} -t test-helpers/*`, rootDir);
-        expect(providenceStub.args[0][1].targetProjectPaths).to.eql([
-          `${process.cwd()}/needed-for-test/pass-glob`,
-        ]);
-      });
+      await runCli(`${analyzeCmd} --search-target-paths /mocked/path/example-project`, rootDir);
+      expect(pathsArrayFromCsStub.args[0][0]).to.equal('/mocked/path/example-project');
+      expect(providenceStub.args[0][1].targetProjectPaths).to.eql(['/mocked/path/example-project']);
     });
 
-    it('"-r", "--reference-paths"', async () => {});
-    it('"--search-target-collection"', async () => {});
-    it('"--reference-collection"', async () => {});
+    it('"-r --reference-paths"', async () => {
+      await runCli(`${analyzeCmd} -r /mocked/path/example-project`, rootDir);
+      expect(pathsArrayFromCsStub.args[0][0]).to.equal('/mocked/path/example-project');
+      expect(providenceStub.args[0][1].referenceProjectPaths).to.eql([
+        '/mocked/path/example-project',
+      ]);
 
-    it.skip('"-R --verbose-report"', async () => {});
-    it.skip('"-D", "--debug"', async () => {});
+      pathsArrayFromCsStub.resetHistory();
+      providenceStub.resetHistory();
+
+      await runCli(`${analyzeCmd} --reference-paths /mocked/path/example-project`, rootDir);
+      expect(pathsArrayFromCsStub.args[0][0]).to.equal('/mocked/path/example-project');
+      expect(providenceStub.args[0][1].referenceProjectPaths).to.eql([
+        '/mocked/path/example-project',
+      ]);
+    });
+
+    it('"--search-target-collection"', async () => {
+      await runCli(`${analyzeCmd} --search-target-collection lion-collection`, rootDir);
+      expect(pathsArrayFromCollectionStub.args[0][0]).to.equal('lion-collection');
+      expect(providenceStub.args[0][1].targetProjectPaths).to.eql(['/mocked/path/example-project']);
+    });
+
+    it('"--reference-collection"', async () => {
+      await runCli(`${analyzeCmd} --reference-collection lion-based-ui-collection`, rootDir);
+      expect(pathsArrayFromCollectionStub.args[0][0]).to.equal('lion-based-ui-collection');
+      expect(providenceStub.args[0][1].referenceProjectPaths).to.eql([
+        '/mocked/path/example-project',
+      ]);
+    });
+
+    it('"-w --whitelist"', async () => {
+      await runCli(`${analyzeCmd} -w /mocked/path/example-project`, rootDir);
+      expect(pathsArrayFromCsStub.args[0][0]).to.equal('/mocked/path/example-project');
+      expect(providenceStub.args[0][1].gatherFilesConfig.filter).to.eql([
+        '/mocked/path/example-project',
+      ]);
+
+      pathsArrayFromCsStub.resetHistory();
+      providenceStub.resetHistory();
+
+      await runCli(`${analyzeCmd} --whitelist /mocked/path/example-project`, rootDir);
+      expect(pathsArrayFromCsStub.args[0][0]).to.equal('/mocked/path/example-project');
+      expect(providenceStub.args[0][1].gatherFilesConfig.filter).to.eql([
+        '/mocked/path/example-project',
+      ]);
+    });
+
+    it('"--whitelist-reference"', async () => {
+      await runCli(`${analyzeCmd} --whitelist-reference /mocked/path/example-project`, rootDir);
+      expect(pathsArrayFromCsStub.args[0][0]).to.equal('/mocked/path/example-project');
+      expect(providenceStub.args[0][1].gatherFilesConfigReference.filter).to.eql([
+        '/mocked/path/example-project',
+      ]);
+    });
+
+    it('"-D --debug"', async () => {
+      await runCli(`${analyzeCmd} -D`, rootDir);
+      expect(providenceStub.args[0][1].debugEnabled).to.equal(true);
+
+      providenceStub.resetHistory();
+
+      await runCli(`${analyzeCmd} --debug`, rootDir);
+      expect(providenceStub.args[0][1].debugEnabled).to.equal(true);
+    });
+
+    it('--write-log-file"', async () => {
+      await runCli(`${analyzeCmd} --write-log-file`, rootDir);
+      expect(providenceStub.args[0][1].writeLogFile).to.equal(true);
+    });
+
+    it('--include-target-deps"', async () => {
+      await runCli(`${analyzeCmd}`, rootDir);
+      expect(appendProjectDependencyPathsStub.called).to.be.false;
+
+      appendProjectDependencyPathsStub.resetHistory();
+      providenceStub.resetHistory();
+
+      await runCli(`${analyzeCmd} --include-target-deps`, rootDir);
+      expect(appendProjectDependencyPathsStub.called).to.be.true;
+      expect(providenceStub.args[0][1].targetProjectPaths).to.eql([
+        '/mocked/path/example-project',
+        '/mocked/path/example-project/node_modules/mock-dep-a',
+        '/mocked/path/example-project/bower_components/mock-dep-b',
+      ]);
+    });
+
+    it('--target-deps-filter"', async () => {
+      await runCli(`${analyzeCmd} --include-target-deps --target-deps-filter ^mock-`, rootDir);
+      expect(appendProjectDependencyPathsStub.args[0][1]).to.equal('^mock-');
+    });
   });
 
   describe('Commands', () => {
     describe('Analyze', () => {
       it('calls providence', async () => {
-        expect(typeof dummyAnalyzer.name).to.equal('string');
+        await runCli(`${analyzeCmd}`, rootDir);
+        expect(providenceStub.called).to.be.true;
       });
+
       describe('Options', () => {
-        it('"-o", "--prompt-optional-config"', async () => {});
-        it('"-c", "--config"', async () => {});
+        it('"-o --prompt-optional-config"', async () => {
+          await runCli(`analyze -o`, rootDir);
+          expect(promptStub.called).to.be.true;
+
+          promptStub.resetHistory();
+
+          await runCli(`analyze --prompt-optional-config`, rootDir);
+          expect(promptStub.called).to.be.true;
+        });
+
+        it('"-c --config"', async () => {
+          await runCli(`analyze mock-analyzer -c {"a":"2"}`, rootDir);
+          expect(qConfStub.args[0][0]).to.equal('mock-analyzer');
+          expect(qConfStub.args[0][1]).to.eql({ a: '2', metaConfig: undefined });
+
+          qConfStub.resetHistory();
+
+          await runCli(`analyze mock-analyzer --config {"a":"2"}`, rootDir);
+          expect(qConfStub.args[0][0]).to.equal('mock-analyzer');
+          expect(qConfStub.args[0][1]).to.eql({ a: '2', metaConfig: undefined });
+        });
+
+        it('calls "promptAnalyzerConfigMenu" without config given', async () => {
+          await runCli(`analyze mock-analyzer`, rootDir);
+          expect(promptCfgStub.called).to.be.true;
+        });
       });
     });
-    describe('Query', () => {});
-    describe('Search', () => {});
+
+    describe.skip('Query', () => {});
+    describe.skip('Search', () => {});
+
     describe('Manage', () => {});
+
     describe('Extend docs', () => {
       let extendDocsStub;
-      beforeEach(() => {
+
+      before(() => {
         extendDocsStub = sinon
           .stub(extendDocsModule, 'launchProvidenceWithExtendDocs')
           .returns(Promise.resolve());
       });
 
-      afterEach(() => {
+      after(() => {
         extendDocsStub.restore();
       });
 
+      afterEach(() => {
+        extendDocsStub.resetHistory();
+      });
+
       it('allows configuration', async () => {
         await runCli(
           [
@@ -176,8 +363,8 @@ describe('Providence CLI', () => {
           },
           outputFolder: '/outp',
           extensions: ['.bla'],
-          whitelist: [`${process.cwd()}/wl`],
-          whitelistReference: [`${process.cwd()}/wlr`],
+          whitelist: [`${rootDir}/wl`],
+          whitelistReference: [`${rootDir}/wlr`],
         });
       });
     });
@@ -203,8 +390,102 @@ describe('CLI helpers', () => {
 
     it('allows globs', async () => {
       expect(pathsArrayFromCs('test-helpers/project-mocks*', rootDir)).to.eql([
-        `${process.cwd()}/test-helpers/project-mocks`,
-        `${process.cwd()}/test-helpers/project-mocks-analyzer-outputs`,
+        `${rootDir}/test-helpers/project-mocks`,
+        `${rootDir}/test-helpers/project-mocks-analyzer-outputs`,
+      ]);
+    });
+
+    it('allows multiple comma separated paths', async () => {
+      const paths =
+        'test-helpers/project-mocks*, ./test-helpers/project-mocks/importing-target-project,/mocked/path/example-project';
+      expect(pathsArrayFromCs(paths, rootDir)).to.eql([
+        `${rootDir}/test-helpers/project-mocks`,
+        `${rootDir}/test-helpers/project-mocks-analyzer-outputs`,
+        `${rootDir}/test-helpers/project-mocks/importing-target-project`,
+        '/mocked/path/example-project',
+      ]);
+    });
+  });
+
+  describe('pathsArrayFromCollectionName', () => {
+    it('gets collections from external target config', async () => {
+      expect(
+        pathsArrayFromCollectionName('lion-collection', 'search-target', externalCfgMock, rootDir),
+      ).to.eql(
+        externalCfgMock.searchTargetCollections['lion-collection'].map(p =>
+          pathLib.join(rootDir, p),
+        ),
+      );
+    });
+
+    it('gets collections from external reference config', async () => {
+      expect(
+        pathsArrayFromCollectionName(
+          'lion-based-ui-collection',
+          'reference',
+          externalCfgMock,
+          rootDir,
+        ),
+      ).to.eql(
+        externalCfgMock.referenceCollections['lion-based-ui-collection'].map(p =>
+          pathLib.join(rootDir, p),
+        ),
+      );
+    });
+  });
+
+  describe('appendProjectDependencyPaths', () => {
+    before(() => {
+      mockWriteToJson(queryResults);
+      suppressNonCriticalLogs();
+
+      mockProject(
+        {
+          './src/OriginalComp.js': `export class OriginalComp {}`,
+          './src/inbetween.js': `export { OriginalComp as InBetweenComp } from './OriginalComp.js'`,
+          './index.js': `export { InBetweenComp as MyComp } from './src/inbetween.js'`,
+          './node_modules/dependency-a/index.js': '',
+          './bower_components/dependency-b/index.js': '',
+        },
+        {
+          projectName: 'example-project',
+          projectPath: '/mocked/path/example-project',
+        },
+      );
+    });
+
+    it('adds bower and node dependencies', async () => {
+      const result = await appendProjectDependencyPaths(['/mocked/path/example-project']);
+      expect(result).to.eql([
+        '/mocked/path/example-project/node_modules/dependency-a',
+        '/mocked/path/example-project/bower_components/dependency-b',
+        '/mocked/path/example-project',
+      ]);
+    });
+
+    it('allows a regex filter', async () => {
+      const result = await appendProjectDependencyPaths(['/mocked/path/example-project'], 'b$');
+      expect(result).to.eql([
+        '/mocked/path/example-project/bower_components/dependency-b',
+        '/mocked/path/example-project',
+      ]);
+    });
+
+    it('allows to filter out only npm or bower deps', async () => {
+      const result = await appendProjectDependencyPaths(['/mocked/path/example-project'], null, [
+        'npm',
+      ]);
+      expect(result).to.eql([
+        '/mocked/path/example-project/node_modules/dependency-a',
+        '/mocked/path/example-project',
+      ]);
+
+      const result2 = await appendProjectDependencyPaths(['/mocked/path/example-project'], null, [
+        'bower',
+      ]);
+      expect(result2).to.eql([
+        '/mocked/path/example-project/bower_components/dependency-b',
+        '/mocked/path/example-project',
       ]);
     });
   });
diff --git a/packages/providence-analytics/test-node/program/services/InputDataService.test.js b/packages/providence-analytics/test-node/program/services/InputDataService.test.js
index 6392cdea3..2a5536168 100644
--- a/packages/providence-analytics/test-node/program/services/InputDataService.test.js
+++ b/packages/providence-analytics/test-node/program/services/InputDataService.test.js
@@ -118,7 +118,7 @@ describe('InputDataService', () => {
         ]);
       });
 
-      it('allows passing excludeFolders', async () => {
+      it('allows passing excluded folders', async () => {
         const globOutput = InputDataService.gatherFilesFromDir('/fictional/project', {
           extensions: ['.html', '.js'],
           filter: ['!nested/**'],