diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 000000000..ccbe84d83
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Contact GitHub Support
+    url: https://support.github.com/contact?subject=Code+Scanning+Beta+Support&tags=code-scanning-support
+    about: Contact Support about code scanning
diff --git a/.github/codeql/codeql-config.yml b/.github/codeql/codeql-config.yml
index 6883bf197..1a3d79a79 100644
--- a/.github/codeql/codeql-config.yml
+++ b/.github/codeql/codeql-config.yml
@@ -2,5 +2,12 @@ name: "CodeQL config"
 queries: 
   - name: Run custom queries
     uses: ./queries
+  # Run all extra query suites, both because we want to
+  # and because it'll act as extra testing. This is why
+  # we include both even though one is a superset of the
+  # other, because we're testing the parsing logic and
+  # that the suites exist in the codeql bundle.
+  - uses: security-extended
+  - uses: security-and-quality
 paths-ignore:
   - tests
\ No newline at end of file
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index 761d70aa5..a3a5831d3 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -1,6 +1,6 @@
 name: "CodeQL action"
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   build:
@@ -11,6 +11,16 @@ jobs:
 
     steps:
     - uses: actions/checkout@v1
+      with:
+        # Must fetch at least the immediate parents so that if this is
+        # a pull request then we can checkout the head of the pull request.
+        fetch-depth: 2
+
+    # If this run was triggered by a pull request event then checkout
+    # the head of the pull request instead of the merge commit.
+    - run: git checkout HEAD^2
+      if: ${{ github.event_name == 'pull_request' }}
+
     - uses: ./init
       with:
         languages: javascript
diff --git a/.github/workflows/integration-testing.yml b/.github/workflows/integration-testing.yml
index e2db985ca..bb6cb4ca1 100644
--- a/.github/workflows/integration-testing.yml
+++ b/.github/workflows/integration-testing.yml
@@ -1,14 +1,10 @@
 name: "Integration Testing"
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   multi-language-repo_test-autodetect-languages:
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest]
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v2
@@ -16,9 +12,8 @@ jobs:
       shell: bash
       run: |
         mkdir ../action
-        shopt -s dotglob
-        mv * ../action/
-        mv ../action/tests/multi-language-repo/* .
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
     - uses: ./../action/init
     - name: Build code
       shell: bash
@@ -26,6 +21,20 @@ jobs:
     - uses: ./../action/analyze
       env:
         TEST_MODE: true
+    - run: |
+        cd "$CODEQL_ACTION_DATABASE_DIR"
+        # List all directories as there will be precisely one directory per database
+        # but there may be other files in this directory such as query suites.
+        if [ "$(ls -d */ | wc -l)" != 6 ] || \
+           [[ ! -d cpp ]] || \
+           [[ ! -d csharp ]] || \
+           [[ ! -d go ]] || \
+           [[ ! -d java ]] || \
+           [[ ! -d javascript ]] || \
+           [[ ! -d python ]]; then
+          echo "Did not find expected number of databases. Database dir contains: $(ls)"
+          exit 1
+        fi
 
   multi-language-repo_test-custom-queries:
     strategy:
@@ -40,9 +49,8 @@ jobs:
       shell: bash
       run: |
         mkdir ../action
-        shopt -s dotglob
-        mv * ../action/
-        mv ../action/tests/multi-language-repo/* .
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
     - uses: ./../action/init
       with:
         languages: cpp,csharp,java,javascript,python
@@ -72,9 +80,8 @@ jobs:
       shell: bash
       run: |
         mkdir ../action
-        shopt -s dotglob
-        mv * ../action/
-        mv ../action/tests/multi-language-repo/* .
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
     - uses: ./../action/init
       with:
         languages: go
@@ -96,9 +103,8 @@ jobs:
       shell: bash
       run: |
         mkdir ../action
-        shopt -s dotglob
-        mv * ../action/
-        mv ../action/tests/multi-language-repo/* .
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
     - name: Set up Ruby
       uses: ruby/setup-ruby@v1
       with:
@@ -117,4 +123,4 @@ jobs:
       with:
         sarif_file: rubocop.sarif
       env:
-        TEST_MODE: true
\ No newline at end of file
+        TEST_MODE: true
diff --git a/README.md b/README.md
index 09e092f1c..382f6a038 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,8 @@ The underlying CodeQL CLI, used in this action, is licensed under the [GitHub Co
 
 ## Usage
 
+This is a short walkthrough, but for more information read [configuring code scanning](https://help.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning).
+
 To get code scanning results from CodeQL analysis on your repo you can use the following workflow as a template:
 
 ```yaml
@@ -18,6 +20,7 @@ name: "Code Scanning - Action"
 
 on:
   push:
+  pull_request:
   schedule:
     - cron: '0 0 * * 0'
 
@@ -33,6 +36,17 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
+        with:
+          # Must fetch at least the immediate parents so that if this is
+          # a pull request then we can checkout the head of the pull request.
+          # Only include this option if you are running this workflow on pull requests.
+          fetch-depth: 2
+
+      # If this run was triggered by a pull request event then checkout
+      # the head of the pull request instead of the merge commit.
+      # Only include this step if you are running this workflow on pull requests.
+      - run: git checkout HEAD^2
+        if: ${{ github.event_name == 'pull_request' }}
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
@@ -78,24 +92,9 @@ If you prefer to integrate this within an existing CI workflow, it should end up
   uses: github/codeql-action/analyze@v1
 ```
 
-### Actions triggers
-
-The CodeQL action should be run on `push` events, and on a `schedule`. `Push` events allow us to do a detailed analysis of the delta in a pull request, while the `schedule` event ensures that GitHub regularly scans the repository for the latest vulnerabilities, even if the repository becomes inactive. This action does not support the `pull_request` event.
-
-### Configuration
-
-You may optionally specify additional queries for CodeQL to execute by using a config file. The queries must belong to a [QL pack](https://help.semmle.com/codeql/codeql-cli/reference/qlpack-overview.html) and can be in your repository or any public repository. You can choose a single .ql file, a folder containing multiple .ql files, a .qls [query suite](https://help.semmle.com/codeql/codeql-cli/procedures/query-suites.html) file, or any combination of the above. To use queries stored in your repository or from other repositories use the same syntax as when [using an action](https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobsjob_idstepsuses). Note that when using local queries starting with `./`, the path is relative to the root of the repository and not to the location of the config file.
+### Configuration file
 
-You can disable the default queries using `disable-default-queries: true`.
-
-You can choose to ignore some files or folders from the analysis, or include additional files/folders for analysis. This *only* works for Javascript and Python analysis.
-Identifying potential files for extraction:
-
-- Scans each folder that's defined as `paths` in turn, traversing subfolders, and looking for relevant files.
-- If it finds a subfolder that's defined as `paths-ignore`, stop traversing.
-- If a file or folder is both in `paths` and `paths-ignore`, the `paths-ignore` is ignored.
-
-Use the `config-file` parameter of the init action to enable the configuration file. For example:
+Use the `config-file` parameter of the `init` action to enable the configuration file. The value of `config-file` is the path to the configuration file you want to use. This example loads the configuration file `./.github/codeql/codeql-config.yml`.
 
 ```yaml
 - uses: github/codeql-action/init@v1
@@ -103,72 +102,8 @@ Use the `config-file` parameter of the init action to enable the configuration f
     config-file: ./.github/codeql/codeql-config.yml
 ```
 
-A config file looks like this:
-
-```yaml
-name: "My CodeQL config"
-
-disable-default-queries: true
-
-queries:
-  - name: In-repo queries (Runs the queries located in the my-queries folder of the repo)
-    uses: ./my-queries
-  - name: External Javascript QL pack (Runs a QL pack located in an external repo)
-    uses: /Semmle/ql/javascript/ql/src/Electron@master
-  - name: External query (Runs a single query located in an external QL pack)
-    uses: Semmle/ql/javascript/ql/src/AngularJS/DeadAngularJSEventListener.ql@master
-  - name: Select query suite (Runs a query suites)
-    uses: ./codeql-querypacks/complex-python-querypack/rootAndBar.qls
-
-paths:
-  - src/util.ts
-
-paths-ignore:
-  - src
-  - lib
-```
+The configuration file must be located within the local repository. For information on how to write a configuration file, see "[Using a custom configuration](https://help.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#using-a-custom-configuration)."
 
 ## Troubleshooting
 
-### Trouble with Go dependencies
-
-#### If you use a vendor directory
-
-Try passing
-
-```yaml
-env:
-  GOFLAGS: "-mod=vendor"
-```
-
-to `github/codeql-action/analyze`.
-
-#### If you do not use a vendor directory
-
-Dependencies on public repositories should just work. If you have dependencies on private repositories, one option is to use `git config` and a [personal access token](https://help.github.com/en/github/authenticating-to-github/creating-a-personal-access-token-for-the-command-line) to authenticate when downloading dependencies. Add a section like
-
-```yaml
-steps:
-  - name: Configure git private repo access
-    env:
-      TOKEN: ${{ secrets.GITHUB_PAT }}
-    run: |
-      git config --global url."https://${TOKEN}@github.com/foo/bar".insteadOf "https://github.com/foo/bar"
-      git config --global url."https://${TOKEN}@github.com/foo/baz".insteadOf "https://github.com/foo/baz"
-```
-
-before any codeql actions. A similar thing can also be done with an SSH key or deploy key.
-
-### C# using dotnet version 2 on linux
-
-This currently requires invoking `dotnet` with the `/p:UseSharedCompilation=false` flag. For example:
-
-```shell
-dotnet build /p:UseSharedCompilation=false
-```
-
-Version 3 does not require the additional flag.
-
-### Analysing Go together with other languages on `macos-latest`
-
-When running on macos it is currently not possible to analyze Go in conjunction with any of Java, C/C++, or C#. Each language can still be analyzed separately.
\ No newline at end of file
+Read about [troubleshooting code scanning](https://help.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/troubleshooting-code-scanning).
diff --git a/init/action.yml b/init/action.yml
index 2a0750d69..2e7c9ee99 100644
--- a/init/action.yml
+++ b/init/action.yml
@@ -5,7 +5,7 @@ inputs:
   tools:
     description: URL of CodeQL tools
     required: false
-    default: https://github.com/github/codeql-action/releases/download/codeql-bundle-20200427/codeql-bundle.tar.gz
+    default: https://github.com/github/codeql-action/releases/download/codeql-bundle-20200601/codeql-bundle.tar.gz
   languages:
     description: The languages to be analysed
     required: false
diff --git a/lib/config-utils.js b/lib/config-utils.js
index f0fd07731..fc6ceddd5 100644
--- a/lib/config-utils.js
+++ b/lib/config-utils.js
@@ -27,12 +27,15 @@ class ExternalQuery {
     }
 }
 exports.ExternalQuery = ExternalQuery;
+// The set of acceptable values for built-in suites from the codeql bundle
+const builtinSuites = ['security-extended', 'security-and-quality'];
 class Config {
     constructor() {
         this.name = "";
         this.disableDefaultQueries = false;
         this.additionalQueries = [];
         this.externalQueries = [];
+        this.additionalSuites = [];
         this.pathsIgnore = [];
         this.paths = [];
     }
@@ -45,9 +48,33 @@ class Config {
         }
         // Check for the local path case before we start trying to parse the repository name
         if (queryUses.startsWith("./")) {
-            this.additionalQueries.push(queryUses.slice(2));
+            const localQueryPath = queryUses.slice(2);
+            // Resolve the local path against the workspace so that when this is
+            // passed to codeql it resolves to exactly the path we expect it to resolve to.
+            const workspacePath = util.getRequiredEnvParam('GITHUB_WORKSPACE');
+            const absoluteQueryPath = path.join(workspacePath, localQueryPath);
+            // Check the file exists
+            if (!fs.existsSync(absoluteQueryPath)) {
+                throw new Error(getLocalPathDoesNotExist(configFile, localQueryPath));
+            }
+            // Check the local path doesn't jump outside the repo using '..' or symlinks
+            if (!(fs.realpathSync(absoluteQueryPath) + path.sep).startsWith(workspacePath + path.sep)) {
+                throw new Error(getLocalPathOutsideOfRepository(configFile, localQueryPath));
+            }
+            this.additionalQueries.push(absoluteQueryPath);
             return;
         }
+        // Check for one of the builtin suites
+        if (queryUses.indexOf('/') === -1 && queryUses.indexOf('@') === -1) {
+            const suite = builtinSuites.find((suite) => suite === queryUses);
+            if (suite) {
+                this.additionalSuites.push(suite);
+                return;
+            }
+            else {
+                throw new Error(getQueryUsesInvalid(configFile, queryUses));
+            }
+        }
         let tok = queryUses.split('@');
         if (tok.length !== 2) {
             throw new Error(getQueryUsesInvalid(configFile, queryUses));
@@ -88,7 +115,8 @@ function getQueriesInvalid(configFile) {
 }
 exports.getQueriesInvalid = getQueriesInvalid;
 function getQueryUsesInvalid(configFile, queryUses) {
-    return getConfigFilePropertyError(configFile, QUERIES_PROPERTY + '.' + QUERIES_USES_PROPERTY, 'must be non-empty string containing either a local path starting with "./", or be of the form "owner/repo[/path]@ref"' +
+    return getConfigFilePropertyError(configFile, QUERIES_PROPERTY + '.' + QUERIES_USES_PROPERTY, 'must be a built-in suite (' + builtinSuites.join(' or ') +
+        '), a relative path, or be of the form "owner/repo[/path]@ref"' +
         (queryUses !== undefined ? '\n Found: ' + queryUses : ''));
 }
 exports.getQueryUsesInvalid = getQueryUsesInvalid;
@@ -100,6 +128,14 @@ function getPathsInvalid(configFile) {
     return getConfigFilePropertyError(configFile, PATHS_PROPERTY, 'must be an array of non-empty string');
 }
 exports.getPathsInvalid = getPathsInvalid;
+function getLocalPathOutsideOfRepository(configFile, localPath) {
+    return getConfigFilePropertyError(configFile, QUERIES_PROPERTY + '.' + QUERIES_USES_PROPERTY, 'is invalid as the local path "' + localPath + '" is output of the repository');
+}
+exports.getLocalPathOutsideOfRepository = getLocalPathOutsideOfRepository;
+function getLocalPathDoesNotExist(configFile, localPath) {
+    return getConfigFilePropertyError(configFile, QUERIES_PROPERTY + '.' + QUERIES_USES_PROPERTY, 'is invalid as the local path "' + localPath + '" does not exist in the repository');
+}
+exports.getLocalPathDoesNotExist = getLocalPathDoesNotExist;
 function getConfigFileOutsideWorkspaceErrorMessage(configFile) {
     return 'The configuration file "' + configFile + '" is outside of the workspace';
 }
diff --git a/lib/config-utils.js.map b/lib/config-utils.js.map
index 444862b46..1ff07eeef 100644
--- a/lib/config-utils.js.map
+++ b/lib/config-utils.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/lib/config-utils.test.js b/lib/config-utils.test.js
index b35069f92..583ed88f3 100644
--- a/lib/config-utils.test.js
+++ b/lib/config-utils.test.js
@@ -87,6 +87,7 @@ ava_1.default("load non-empty input", async (t) => {
       name: my config
       disable-default-queries: true
       queries:
+        - uses: ./
         - uses: ./foo
         - uses: foo/bar@dev
       paths-ignore:
@@ -98,12 +99,14 @@ ava_1.default("load non-empty input", async (t) => {
         const expectedConfig = new configUtils.Config();
         expectedConfig.name = 'my config';
         expectedConfig.disableDefaultQueries = true;
-        expectedConfig.additionalQueries.push('foo');
+        expectedConfig.additionalQueries.push(tmpDir);
+        expectedConfig.additionalQueries.push(path.join(tmpDir, 'foo'));
         expectedConfig.externalQueries = [new configUtils.ExternalQuery('foo/bar', 'dev')];
         expectedConfig.pathsIgnore = ['a', 'b'];
         expectedConfig.paths = ['c/d'];
         fs.writeFileSync(path.join(tmpDir, 'input'), inputFileContents, 'utf8');
         setInput('config-file', 'input');
+        fs.mkdirSync(path.join(tmpDir, 'foo'));
         const actualConfig = await configUtils.loadConfig();
         // Should exactly equal the object we constructed earlier
         t.deepEqual(actualConfig, expectedConfig);
@@ -138,7 +141,7 @@ doInvalidInputTest('queries uses invalid type', `
   queries:
   - uses:
       - hello: world`, configUtils.getQueryUsesInvalid);
-function doInvalidQueryUsesTest(input, inputInErrorMessage) {
+function doInvalidQueryUsesTest(input, expectedErrorMessageGenerator) {
     // Invalid contents of a "queries.uses" field.
     // Should fail with the expected error message
     const inputFileContents = `
@@ -146,12 +149,14 @@ function doInvalidQueryUsesTest(input, inputInErrorMessage) {
     queries:
       - name: foo
         uses: ` + input;
-    doInvalidInputTest("queries uses \"" + input + "\"", inputFileContents, configFile => configUtils.getQueryUsesInvalid(configFile, inputInErrorMessage ? input : undefined));
+    doInvalidInputTest("queries uses \"" + input + "\"", inputFileContents, expectedErrorMessageGenerator);
 }
 // Various "uses" fields, and the errors they should produce
-doInvalidQueryUsesTest("''", false);
-doInvalidQueryUsesTest("foo/bar", true);
-doInvalidQueryUsesTest("foo/bar@v1@v2", true);
-doInvalidQueryUsesTest("foo@master", true);
-doInvalidQueryUsesTest("https://github.com/foo/bar@master", true);
+doInvalidQueryUsesTest("''", c => configUtils.getQueryUsesInvalid(c, undefined));
+doInvalidQueryUsesTest("foo/bar", c => configUtils.getQueryUsesInvalid(c, "foo/bar"));
+doInvalidQueryUsesTest("foo/bar@v1@v2", c => configUtils.getQueryUsesInvalid(c, "foo/bar@v1@v2"));
+doInvalidQueryUsesTest("foo@master", c => configUtils.getQueryUsesInvalid(c, "foo@master"));
+doInvalidQueryUsesTest("https://github.com/foo/bar@master", c => configUtils.getQueryUsesInvalid(c, "https://github.com/foo/bar@master"));
+doInvalidQueryUsesTest("./foo", c => configUtils.getLocalPathDoesNotExist(c, "foo"));
+doInvalidQueryUsesTest("./..", c => configUtils.getLocalPathOutsideOfRepository(c, ".."));
 //# sourceMappingURL=config-utils.test.js.map
\ No newline at end of file
diff --git a/lib/config-utils.test.js.map b/lib/config-utils.test.js.map
index 00ae67287..74d7519a3 100644
--- a/lib/config-utils.test.js.map
+++ b/lib/config-utils.test.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/lib/finalize-db.js b/lib/finalize-db.js
index 99f5ea7f3..0207bda13 100644
--- a/lib/finalize-db.js
+++ b/lib/finalize-db.js
@@ -67,26 +67,50 @@ async function finalizeDatabaseCreation(codeqlCmd, databaseFolder) {
         core.endGroup();
     }
 }
+async function runResolveQueries(codeqlCmd, queries) {
+    let output = '';
+    const options = {
+        listeners: {
+            stdout: (data) => {
+                output += data.toString();
+            }
+        }
+    };
+    await exec.exec(codeqlCmd, [
+        'resolve',
+        'queries',
+        ...queries,
+        '--format=bylanguage'
+    ], options);
+    return JSON.parse(output);
+}
 async function resolveQueryLanguages(codeqlCmd, config) {
     let res = new Map();
-    if (config.additionalQueries.length !== 0) {
-        let resolveQueriesOutput = '';
-        const options = {
-            listeners: {
-                stdout: (data) => {
-                    resolveQueriesOutput += data.toString();
-                }
+    if (!config.disableDefaultQueries || config.additionalSuites.length !== 0) {
+        const suites = [];
+        for (const language of await util.getLanguages()) {
+            if (!config.disableDefaultQueries) {
+                suites.push(language + '-code-scanning.qls');
             }
-        };
-        await exec.exec(codeqlCmd, [
-            'resolve',
-            'queries',
-            ...config.additionalQueries,
-            '--format=bylanguage'
-        ], options);
-        const resolveQueriesOutputObject = JSON.parse(resolveQueriesOutput);
+            for (const additionalSuite of config.additionalSuites) {
+                suites.push(language + '-' + additionalSuite + '.qls');
+            }
+        }
+        const resolveQueriesOutputObject = await runResolveQueries(codeqlCmd, suites);
         for (const [language, queries] of Object.entries(resolveQueriesOutputObject.byLanguage)) {
-            res[language] = Object.keys(queries);
+            if (res[language] === undefined) {
+                res[language] = [];
+            }
+            res[language].push(...Object.keys(queries));
+        }
+    }
+    if (config.additionalQueries.length !== 0) {
+        const resolveQueriesOutputObject = await runResolveQueries(codeqlCmd, config.additionalQueries);
+        for (const [language, queries] of Object.entries(resolveQueriesOutputObject.byLanguage)) {
+            if (res[language] === undefined) {
+                res[language] = [];
+            }
+            res[language].push(...Object.keys(queries));
         }
         const noDeclaredLanguage = resolveQueriesOutputObject.noDeclaredLanguage;
         const noDeclaredLanguageQueries = Object.keys(noDeclaredLanguage);
@@ -106,11 +130,16 @@ async function runQueries(codeqlCmd, databaseFolder, sarifFolder, config) {
     const queriesPerLanguage = await resolveQueryLanguages(codeqlCmd, config);
     for (let database of fs.readdirSync(databaseFolder)) {
         core.startGroup('Analyzing ' + database);
-        const queries = [];
-        if (!config.disableDefaultQueries) {
-            queries.push(database + '-code-scanning.qls');
+        const queries = queriesPerLanguage[database] || [];
+        if (queries.length === 0) {
+            throw new Error('Unable to analyse ' + database + ' as no queries were selected for this language');
         }
-        queries.push(...(queriesPerLanguage[database] || []));
+        // Pass the queries to codeql using a file instead of using the command
+        // line to avoid command line length restrictions, particularly on windows.
+        const querySuite = path.join(databaseFolder, database + '-queries.qls');
+        const querySuiteContents = queries.map(q => '- query: ' + q).join('\n');
+        fs.writeFileSync(querySuite, querySuiteContents);
+        core.debug('Query suite file for ' + database + '...\n' + querySuiteContents);
         const sarifFile = path.join(sarifFolder, database + '.sarif');
         await exec.exec(codeqlCmd, [
             'database',
@@ -120,7 +149,7 @@ async function runQueries(codeqlCmd, databaseFolder, sarifFolder, config) {
             '--format=sarif-latest',
             '--output=' + sarifFile,
             '--no-sarif-add-snippets',
-            ...queries
+            querySuite
         ]);
         core.debug('SARIF results for database ' + database + ' created at "' + sarifFile + '"');
         core.endGroup();
diff --git a/lib/finalize-db.js.map b/lib/finalize-db.js.map
index 50b3c0923..5da86defe 100644
--- a/lib/finalize-db.js.map
+++ b/lib/finalize-db.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index 19b9e685a..af4e1a3fe 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -133,7 +133,7 @@ async function uploadFiles(sarifFiles) {
             return false;
         }
         core.exportVariable(sentinelEnvVar, sentinelEnvVar);
-        const commitOid = util.getRequiredEnvParam('GITHUB_SHA');
+        const commitOid = await util.getCommitOid();
         const workflowRunIDStr = util.getRequiredEnvParam('GITHUB_RUN_ID');
         const ref = util.getRef();
         const analysisKey = await util.getAnalysisKey();
diff --git a/lib/upload-lib.js.map b/lib/upload-lib.js.map
index 55db2311d..be05da3dd 100644
--- a/lib/upload-lib.js.map
+++ b/lib/upload-lib.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/lib/util.js b/lib/util.js
index 16cd362f9..adf4aa365 100644
--- a/lib/util.js
+++ b/lib/util.js
@@ -11,6 +11,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const core = __importStar(require("@actions/core"));
+const exec = __importStar(require("@actions/exec"));
 const http = __importStar(require("@actions/http-client"));
 const auth = __importStar(require("@actions/http-client/auth"));
 const octokit = __importStar(require("@octokit/rest"));
@@ -33,12 +34,6 @@ function should_abort(actionName, requireInitActionHasRun) {
         core.setFailed('GITHUB_REF must be set.');
         return true;
     }
-    // Should abort if called on a merge commit for a pull request.
-    if (ref.startsWith('refs/pull/')) {
-        core.warning('The CodeQL ' + actionName + ' action is intended for workflows triggered on `push` events, '
-            + 'but the current workflow is running on a pull request. Aborting.');
-        return true;
-    }
     // If the init action is required, then check the it completed successfully.
     if (requireInitActionHasRun && process.env[sharedEnv.CODEQL_ACTION_INIT_COMPLETED] === undefined) {
         core.setFailed('The CodeQL ' + actionName + ' action cannot be used unless the CodeQL init action is run first. Aborting.');
@@ -151,6 +146,21 @@ async function getLanguages() {
     return languages;
 }
 exports.getLanguages = getLanguages;
+/**
+ * Gets the SHA of the commit that is currently checked out.
+ */
+async function getCommitOid() {
+    let commitOid = '';
+    await exec.exec('git', ['rev-parse', 'HEAD'], {
+        silent: true,
+        listeners: {
+            stdout: (data) => { commitOid += data.toString(); },
+            stderr: (data) => { process.stderr.write(data); }
+        }
+    });
+    return commitOid.trim();
+}
+exports.getCommitOid = getCommitOid;
 /**
  * Get the path of the currently executing workflow.
  */
@@ -196,8 +206,20 @@ exports.getAnalysisKey = getAnalysisKey;
  * Get the ref currently being analyzed.
  */
 function getRef() {
-    // it's in the form "refs/heads/master"
-    return getRequiredEnvParam('GITHUB_REF');
+    // Will be in the form "refs/heads/master" on a push event
+    // or in the form "refs/pull/N/merge" on a pull_request event
+    const ref = getRequiredEnvParam('GITHUB_REF');
+    // For pull request refs we want to convert from the 'merge' ref
+    // to the 'head' ref, as that is what we want to analyse.
+    // There should have been some code earlier in the workflow to do
+    // the checkout, but we have no way of verifying that here.
+    const pull_ref_regex = /refs\/pull\/(\d+)\/merge/;
+    if (pull_ref_regex.test(ref)) {
+        return ref.replace(pull_ref_regex, 'refs/pull/$1/head');
+    }
+    else {
+        return ref;
+    }
 }
 exports.getRef = getRef;
 /**
diff --git a/lib/util.js.map b/lib/util.js.map
index 6e83d9e68..0711f51fc 100644
--- a/lib/util.js.map
+++ b/lib/util.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 66dc51a0f..f100a5842 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -91,6 +91,7 @@ test("load non-empty input", async t => {
       name: my config
       disable-default-queries: true
       queries:
+        - uses: ./
         - uses: ./foo
         - uses: foo/bar@dev
       paths-ignore:
@@ -103,7 +104,8 @@ test("load non-empty input", async t => {
     const expectedConfig = new configUtils.Config();
     expectedConfig.name = 'my config';
     expectedConfig.disableDefaultQueries = true;
-    expectedConfig.additionalQueries.push('foo');
+    expectedConfig.additionalQueries.push(tmpDir);
+    expectedConfig.additionalQueries.push(path.join(tmpDir, 'foo'));
     expectedConfig.externalQueries = [new configUtils.ExternalQuery('foo/bar', 'dev')];
     expectedConfig.pathsIgnore = ['a', 'b'];
     expectedConfig.paths = ['c/d'];
@@ -111,6 +113,8 @@ test("load non-empty input", async t => {
     fs.writeFileSync(path.join(tmpDir, 'input'), inputFileContents, 'utf8');
     setInput('config-file', 'input');
 
+    fs.mkdirSync(path.join(tmpDir, 'foo'));
+
     const actualConfig = await configUtils.loadConfig();
 
     // Should exactly equal the object we constructed earlier
@@ -177,7 +181,10 @@ doInvalidInputTest(
       - hello: world`,
   configUtils.getQueryUsesInvalid);
 
-function doInvalidQueryUsesTest(input: string, inputInErrorMessage: boolean) {
+function doInvalidQueryUsesTest(
+  input: string,
+  expectedErrorMessageGenerator: (configFile: string) => string) {
+
   // Invalid contents of a "queries.uses" field.
   // Should fail with the expected error message
   const inputFileContents = `
@@ -189,14 +196,28 @@ function doInvalidQueryUsesTest(input: string, inputInErrorMessage: boolean) {
   doInvalidInputTest(
     "queries uses \"" + input + "\"",
     inputFileContents,
-    configFile => configUtils.getQueryUsesInvalid(
-      configFile,
-      inputInErrorMessage ? input : undefined));
+    expectedErrorMessageGenerator);
 }
 
 // Various "uses" fields, and the errors they should produce
-doInvalidQueryUsesTest("''", false);
-doInvalidQueryUsesTest("foo/bar", true);
-doInvalidQueryUsesTest("foo/bar@v1@v2", true);
-doInvalidQueryUsesTest("foo@master", true);
-doInvalidQueryUsesTest("https://github.com/foo/bar@master", true);
+doInvalidQueryUsesTest(
+  "''",
+  c => configUtils.getQueryUsesInvalid(c, undefined));
+doInvalidQueryUsesTest(
+  "foo/bar",
+  c => configUtils.getQueryUsesInvalid(c, "foo/bar"));
+doInvalidQueryUsesTest(
+  "foo/bar@v1@v2",
+  c => configUtils.getQueryUsesInvalid(c, "foo/bar@v1@v2"));
+doInvalidQueryUsesTest(
+  "foo@master",
+  c => configUtils.getQueryUsesInvalid(c, "foo@master"));
+doInvalidQueryUsesTest(
+  "https://github.com/foo/bar@master",
+  c => configUtils.getQueryUsesInvalid(c, "https://github.com/foo/bar@master"));
+doInvalidQueryUsesTest(
+  "./foo",
+  c => configUtils.getLocalPathDoesNotExist(c, "foo"));
+doInvalidQueryUsesTest(
+  "./..",
+  c => configUtils.getLocalPathOutsideOfRepository(c, ".."));
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 11a21d884..80f7f9bd2 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -24,11 +24,17 @@ export class ExternalQuery {
     }
 }
 
+// The set of acceptable values for built-in suites from the codeql bundle
+const builtinSuites = ['security-extended', 'security-and-quality'] as const;
+// Derive the union type from the array values
+type BuiltInSuite = typeof builtinSuites[number];
+
 export class Config {
     public name = "";
     public disableDefaultQueries = false;
     public additionalQueries: string[] = [];
     public externalQueries: ExternalQuery[] = [];
+    public additionalSuites: BuiltInSuite[] = [];
     public pathsIgnore: string[] = [];
     public paths: string[] = [];
 
@@ -42,10 +48,37 @@ export class Config {
 
         // Check for the local path case before we start trying to parse the repository name
         if (queryUses.startsWith("./")) {
-            this.additionalQueries.push(queryUses.slice(2));
+            const localQueryPath = queryUses.slice(2);
+            // Resolve the local path against the workspace so that when this is
+            // passed to codeql it resolves to exactly the path we expect it to resolve to.
+            const workspacePath = util.getRequiredEnvParam('GITHUB_WORKSPACE');
+            const absoluteQueryPath = path.join(workspacePath, localQueryPath);
+
+            // Check the file exists
+            if (!fs.existsSync(absoluteQueryPath)) {
+                throw new Error(getLocalPathDoesNotExist(configFile, localQueryPath));
+            }
+
+            // Check the local path doesn't jump outside the repo using '..' or symlinks
+            if (!(fs.realpathSync(absoluteQueryPath) + path.sep).startsWith(workspacePath + path.sep)) {
+                throw new Error(getLocalPathOutsideOfRepository(configFile, localQueryPath));
+            }
+
+            this.additionalQueries.push(absoluteQueryPath);
             return;
         }
 
+        // Check for one of the builtin suites
+        if (queryUses.indexOf('/') === -1 && queryUses.indexOf('@') === -1) {
+            const suite = builtinSuites.find((suite) => suite === queryUses);
+            if (suite) {
+                this.additionalSuites.push(suite);
+                return;
+            } else {
+                throw new Error(getQueryUsesInvalid(configFile, queryUses));
+            }
+        }
+
         let tok = queryUses.split('@');
         if (tok.length !== 2) {
             throw new Error(getQueryUsesInvalid(configFile, queryUses));
@@ -92,7 +125,8 @@ export function getQueryUsesInvalid(configFile: string, queryUses?: string): str
     return getConfigFilePropertyError(
         configFile,
         QUERIES_PROPERTY + '.' + QUERIES_USES_PROPERTY,
-        'must be non-empty string containing either a local path starting with "./", or be of the form "owner/repo[/path]@ref"' +
+        'must be a built-in suite (' + builtinSuites.join(' or ') +
+            '), a relative path, or be of the form "owner/repo[/path]@ref"' +
             (queryUses !== undefined ? '\n Found: ' + queryUses : ''));
 }
 
@@ -104,6 +138,20 @@ export function getPathsInvalid(configFile: string): string {
     return getConfigFilePropertyError(configFile, PATHS_PROPERTY, 'must be an array of non-empty string');
 }
 
+export function getLocalPathOutsideOfRepository(configFile: string, localPath: string): string {
+    return getConfigFilePropertyError(
+        configFile,
+        QUERIES_PROPERTY + '.' + QUERIES_USES_PROPERTY,
+        'is invalid as the local path "' + localPath + '" is output of the repository');
+}
+
+export function getLocalPathDoesNotExist(configFile: string, localPath: string): string {
+    return getConfigFilePropertyError(
+        configFile,
+        QUERIES_PROPERTY + '.' + QUERIES_USES_PROPERTY,
+        'is invalid as the local path "' + localPath + '" does not exist in the repository');
+}
+
 export function getConfigFileOutsideWorkspaceErrorMessage(configFile: string): string {
     return 'The configuration file "' + configFile + '" is outside of the workspace';
 }
diff --git a/src/finalize-db.ts b/src/finalize-db.ts
index a49bb7852..8dfa29226 100644
--- a/src/finalize-db.ts
+++ b/src/finalize-db.ts
@@ -69,32 +69,74 @@ async function finalizeDatabaseCreation(codeqlCmd: string, databaseFolder: strin
   }
 }
 
+interface ResolveQueriesOutput {
+  byLanguage: {
+    [language: string]: {
+      [queryPath: string]: {}
+    }
+  };
+  noDeclaredLanguage: {
+    [queryPath: string]: {}
+  };
+  multipleDeclaredLanguages: {
+    [queryPath: string]: {}
+  };
+}
+
+async function runResolveQueries(codeqlCmd: string, queries: string[]): Promise<ResolveQueriesOutput> {
+  let output = '';
+  const options = {
+    listeners: {
+      stdout: (data: Buffer) => {
+        output += data.toString();
+      }
+    }
+  };
+
+  await exec.exec(
+    codeqlCmd, [
+      'resolve',
+      'queries',
+      ...queries,
+      '--format=bylanguage'
+    ],
+    options);
+
+  return JSON.parse(output);
+}
+
 async function resolveQueryLanguages(codeqlCmd: string, config: configUtils.Config): Promise<Map<string, string[]>> {
   let res = new Map();
 
-  if (config.additionalQueries.length !== 0) {
-    let resolveQueriesOutput = '';
-    const options = {
-      listeners: {
-        stdout: (data: Buffer) => {
-          resolveQueriesOutput += data.toString();
-        }
+  if (!config.disableDefaultQueries || config.additionalSuites.length !== 0) {
+    const suites: string[] = [];
+    for (const language of await util.getLanguages()) {
+      if (!config.disableDefaultQueries) {
+        suites.push(language + '-code-scanning.qls');
+      }
+      for (const additionalSuite of config.additionalSuites) {
+        suites.push(language + '-' + additionalSuite + '.qls');
       }
-    };
+    }
 
-    await exec.exec(
-      codeqlCmd, [
-        'resolve',
-        'queries',
-        ...config.additionalQueries,
-        '--format=bylanguage'
-      ],
-      options);
+    const resolveQueriesOutputObject = await runResolveQueries(codeqlCmd, suites);
 
-    const resolveQueriesOutputObject = JSON.parse(resolveQueriesOutput);
+    for (const [language, queries] of Object.entries(resolveQueriesOutputObject.byLanguage)) {
+      if (res[language] === undefined) {
+        res[language] = [];
+      }
+      res[language].push(...Object.keys(<any>queries));
+    }
+  }
+
+  if (config.additionalQueries.length !== 0) {
+    const resolveQueriesOutputObject = await runResolveQueries(codeqlCmd, config.additionalQueries);
 
     for (const [language, queries] of Object.entries(resolveQueriesOutputObject.byLanguage)) {
-      res[language] = Object.keys(<any>queries);
+      if (res[language] === undefined) {
+        res[language] = [];
+      }
+      res[language].push(...Object.keys(<any>queries));
     }
 
     const noDeclaredLanguage = resolveQueriesOutputObject.noDeclaredLanguage;
@@ -120,11 +162,17 @@ async function runQueries(codeqlCmd: string, databaseFolder: string, sarifFolder
   for (let database of fs.readdirSync(databaseFolder)) {
     core.startGroup('Analyzing ' + database);
 
-    const queries: string[] = [];
-    if (!config.disableDefaultQueries) {
-      queries.push(database + '-code-scanning.qls');
+    const queries = queriesPerLanguage[database] || [];
+    if (queries.length === 0) {
+      throw new Error('Unable to analyse ' + database + ' as no queries were selected for this language');
     }
-    queries.push(...(queriesPerLanguage[database] || []));
+
+    // Pass the queries to codeql using a file instead of using the command
+    // line to avoid command line length restrictions, particularly on windows.
+    const querySuite = path.join(databaseFolder, database + '-queries.qls');
+    const querySuiteContents = queries.map(q => '- query: ' + q).join('\n');
+    fs.writeFileSync(querySuite, querySuiteContents);
+    core.debug('Query suite file for ' + database + '...\n' + querySuiteContents);
 
     const sarifFile = path.join(sarifFolder, database + '.sarif');
 
@@ -136,7 +184,7 @@ async function runQueries(codeqlCmd: string, databaseFolder: string, sarifFolder
       '--format=sarif-latest',
       '--output=' + sarifFile,
       '--no-sarif-add-snippets',
-      ...queries
+      querySuite
     ]);
 
     core.debug('SARIF results for database ' + database + ' created at "' + sarifFile + '"');
diff --git a/src/upload-lib.ts b/src/upload-lib.ts
index 0db8ee40b..fa1b52a77 100644
--- a/src/upload-lib.ts
+++ b/src/upload-lib.ts
@@ -136,7 +136,7 @@ async function uploadFiles(sarifFiles: string[]): Promise<boolean> {
         }
         core.exportVariable(sentinelEnvVar, sentinelEnvVar);
 
-        const commitOid = util.getRequiredEnvParam('GITHUB_SHA');
+        const commitOid = await util.getCommitOid();
         const workflowRunIDStr = util.getRequiredEnvParam('GITHUB_RUN_ID');
         const ref = util.getRef();
         const analysisKey = await util.getAnalysisKey();
diff --git a/src/util.ts b/src/util.ts
index a236216b8..bb133295d 100644
--- a/src/util.ts
+++ b/src/util.ts
@@ -1,4 +1,5 @@
 import * as core from '@actions/core';
+import * as exec from '@actions/exec';
 import * as http from '@actions/http-client';
 import * as auth from '@actions/http-client/auth';
 import * as octokit from '@octokit/rest';
@@ -25,13 +26,6 @@ export function should_abort(actionName: string, requireInitActionHasRun: boolea
         return true;
     }
 
-    // Should abort if called on a merge commit for a pull request.
-    if (ref.startsWith('refs/pull/')) {
-        core.warning('The CodeQL ' + actionName + ' action is intended for workflows triggered on `push` events, '
-            + 'but the current workflow is running on a pull request. Aborting.');
-        return true;
-    }
-
     // If the init action is required, then check the it completed successfully.
     if (requireInitActionHasRun && process.env[sharedEnv.CODEQL_ACTION_INIT_COMPLETED] === undefined) {
         core.setFailed('The CodeQL ' + actionName + ' action cannot be used unless the CodeQL init action is run first. Aborting.');
@@ -152,6 +146,21 @@ export async function getLanguages(): Promise<string[]> {
     return languages;
 }
 
+/**
+ * Gets the SHA of the commit that is currently checked out.
+ */
+export async function getCommitOid(): Promise<string> {
+    let commitOid = '';
+    await exec.exec('git', ['rev-parse', 'HEAD'], {
+        silent: true,
+        listeners: {
+            stdout: (data) => { commitOid += data.toString(); },
+            stderr: (data) => { process.stderr.write(data); }
+        }
+    });
+    return commitOid.trim();
+}
+
 /**
  * Get the path of the currently executing workflow.
  */
@@ -204,8 +213,20 @@ export async function getAnalysisKey(): Promise<string> {
  * Get the ref currently being analyzed.
  */
 export function getRef(): string {
-    // it's in the form "refs/heads/master"
-    return getRequiredEnvParam('GITHUB_REF');
+    // Will be in the form "refs/heads/master" on a push event
+    // or in the form "refs/pull/N/merge" on a pull_request event
+    const ref = getRequiredEnvParam('GITHUB_REF');
+
+    // For pull request refs we want to convert from the 'merge' ref
+    // to the 'head' ref, as that is what we want to analyse.
+    // There should have been some code earlier in the workflow to do
+    // the checkout, but we have no way of verifying that here.
+    const pull_ref_regex = /refs\/pull\/(\d+)\/merge/;
+    if (pull_ref_regex.test(ref)) {
+        return ref.replace(pull_ref_regex, 'refs/pull/$1/head');
+    } else {
+        return ref;
+    }
 }
 
 interface StatusReport {