diff --git a/.flake8 b/.flake8
index 195c783726..04ca460eeb 100644
--- a/.flake8
+++ b/.flake8
@@ -30,3 +30,36 @@
 [flake8]
 ignore = E129,E221,E241,E272,E731,W503,W504,F999,N801,N813,N814
 max-line-length = 79
+
+# F4: Import
+# - F405: `name` may be undefined, or undefined from star imports: `module`
+#
+# F8: Name
+# - F821: undefined name `name`
+#
+per-file-ignores =
+  var/spack/repos/*/package.py:F405,F821
+
+# exclude things we usually do not want linting for.
+# These still get linted when passed explicitly, as when spack flake8 passes
+# them on the command line.
+exclude =
+  .git
+  etc/
+  opt/
+  share/
+  var/spack/cache/
+  var/spack/gpg*/
+  var/spack/junit-report/
+  var/spack/mock-configs/
+  lib/spack/external
+  __pycache__
+  var
+
+format = spack
+
+[flake8:local-plugins]
+report =
+  spack = flake8_formatter:SpackFormatter
+paths =
+  ./share/spack/qa/
diff --git a/.flake8_packages b/.flake8_packages
deleted file mode 100644
index fc2dbf98af..0000000000
--- a/.flake8_packages
+++ /dev/null
@@ -1,24 +0,0 @@
-# -*- conf -*-
-# flake8 settings for Spack package files.
-#
-# This should include all the same exceptions that we use for core files.
-#
-# In Spack packages, we also allow the single `from spack import *`
-# wildcard import and dependencies can set globals for their
-# dependents. So we add exceptions for checks related to undefined names.
-#
-# Note that we also add *per-line* exemptions for certain patterns in the
-# `spack flake8` command.  This is where F403 for `from spack import *`
-# is added (because we *only* allow that wildcard).
-#
-# See .flake8 for regular exceptions.
-#
-# F4: Import
-# - F405: `name` may be undefined, or undefined from star imports: `module`
-#
-# F8: Name
-# - F821: undefined name `name`
-#
-[flake8]
-ignore = E129,E221,E241,E272,E731,W503,W504,F405,F821,F999,N801,N813,N814
-max-line-length = 79
diff --git a/lib/spack/spack/cmd/flake8.py b/lib/spack/spack/cmd/flake8.py
index cdfce2cab2..ce6dbfed20 100644
--- a/lib/spack/spack/cmd/flake8.py
+++ b/lib/spack/spack/cmd/flake8.py
@@ -5,14 +5,19 @@
 
 from __future__ import print_function
 
+try:
+    from itertools import zip_longest  # novm
+except ImportError:
+    from itertools import izip_longest  # novm
+
+    zip_longest = izip_longest
+
 import re
 import os
 import sys
-import shutil
-import tempfile
 import argparse
 
-from llnl.util.filesystem import working_dir, mkdirp
+from llnl.util.filesystem import working_dir
 
 import spack.paths
 from spack.util.executable import which
@@ -23,6 +28,13 @@
 level = "long"
 
 
+def grouper(iterable, n, fillvalue=None):
+    "Collect data into fixed-length chunks or blocks"
+    # grouper('ABCDEFG', 3, 'x') --> ABC DEF Gxx"
+    args = [iter(iterable)] * n
+    return zip_longest(*args, fillvalue=fillvalue)
+
+
 def is_package(f):
     """Whether flake8 should consider a file as a core file or a package.
 
@@ -30,7 +42,7 @@ def is_package(f):
     packages, since we allow `from spack import *` and poking globals
     into packages.
     """
-    return f.startswith('var/spack/repos/') or 'docs/tutorial/examples' in f
+    return f.startswith("var/spack/repos/") or "docs/tutorial/examples" in f
 
 
 #: List of directories to exclude from checks.
@@ -39,96 +51,43 @@ def is_package(f):
 #: max line length we're enforcing (note: this duplicates what's in .flake8)
 max_line_length = 79
 
-#: This is a dict that maps:
-#:  filename pattern ->
-#:     flake8 exemption code ->
-#:        list of patterns, for which matching lines should have codes applied.
-#:
-#: For each file, if the filename pattern matches, we'll add per-line
-#: exemptions if any patterns in the sub-dict match.
-pattern_exemptions = {
-    # exemptions applied only to package.py files.
-    r'package.py$': {
-        # Allow 'from spack import *' in packages, but no other wildcards
-        'F403': [
-            r'^from spack import \*$'
-        ],
-        # Exempt lines with urls and descriptions from overlong line errors.
-        'E501': [
-            r'^\s*homepage\s*=',
-            r'^\s*url\s*=',
-            r'^\s*git\s*=',
-            r'^\s*svn\s*=',
-            r'^\s*hg\s*=',
-            r'^\s*list_url\s*=',
-            r'^\s*version\(',
-            r'^\s*variant\(',
-            r'^\s*provides\(',
-            r'^\s*extends\(',
-            r'^\s*depends_on\(',
-            r'^\s*conflicts\(',
-            r'^\s*resource\(',
-            r'^\s*patch\(',
-        ],
-        # Exempt '@when' decorated functions from redefinition errors.
-        'F811': [
-            r'^\s*@when\(.*\)',
-        ],
-    },
-
-    # exemptions applied to all files.
-    r'.py$': {
-        'E501': [
-            r'(https?|ftp|file)\:',        # URLs
-            r'([\'"])[0-9a-fA-F]{32,}\1',  # long hex checksums
-        ]
-    },
-}
-
-# compile all regular expressions.
-pattern_exemptions = dict(
-    (re.compile(file_pattern),
-     dict((code, [re.compile(p) for p in patterns])
-          for code, patterns in error_dict.items()))
-    for file_pattern, error_dict in pattern_exemptions.items())
-
 
 def changed_files(base=None, untracked=True, all_files=False):
     """Get list of changed files in the Spack repository."""
 
-    git = which('git', required=True)
+    git = which("git", required=True)
 
     if base is None:
-        base = os.environ.get('TRAVIS_BRANCH', 'develop')
+        base = os.environ.get("TRAVIS_BRANCH", "develop")
 
     range = "{0}...".format(base)
 
     git_args = [
         # Add changed files committed since branching off of develop
-        ['diff', '--name-only', '--diff-filter=ACMR', range],
+        ["diff", "--name-only", "--diff-filter=ACMR", range],
         # Add changed files that have been staged but not yet committed
-        ['diff', '--name-only', '--diff-filter=ACMR', '--cached'],
+        ["diff", "--name-only", "--diff-filter=ACMR", "--cached"],
         # Add changed files that are unstaged
-        ['diff', '--name-only', '--diff-filter=ACMR'],
+        ["diff", "--name-only", "--diff-filter=ACMR"],
     ]
 
     # Add new files that are untracked
     if untracked:
-        git_args.append(['ls-files', '--exclude-standard', '--other'])
+        git_args.append(["ls-files", "--exclude-standard", "--other"])
 
     # add everything if the user asked for it
     if all_files:
-        git_args.append(['ls-files', '--exclude-standard'])
+        git_args.append(["ls-files", "--exclude-standard"])
 
     excludes = [os.path.realpath(f) for f in exclude_directories]
     changed = set()
 
     for arg_list in git_args:
-        files = git(*arg_list, output=str).split('\n')
+        files = git(*arg_list, output=str).split("\n")
 
         for f in files:
             # Ignore non-Python files
-            if not (f.endswith('.py') or f == 'bin/spack'):
+            if not (f.endswith(".py") or f == "bin/spack"):
                 continue
 
             # Ignore files in the exclude locations
@@ -140,182 +99,106 @@ def changed_files(base=None, untracked=True, all_files=False):
     return sorted(changed)
 
 
-def add_pattern_exemptions(line, codes):
-    """Add a flake8 exemption to a line."""
-    if line.startswith('#'):
-        return line
-
-    line = line.rstrip('\n')
-
-    # Line is already ignored
-    if line.endswith('# noqa'):
-        return line + '\n'
-
-    orig_len = len(line)
-    codes = set(codes)
-
-    # don't add E501 unless the line is actually too long, as it can mask
-    # other errors like trailing whitespace
-    if orig_len <= max_line_length and "E501" in codes:
-        codes.remove("E501")
-        if not codes:
-            return line + "\n"
-
-    exemptions = ','.join(sorted(codes))
-
-    # append exemption to line
-    if '# noqa: ' in line:
-        line += ',{0}'.format(exemptions)
-    elif line:  # ignore noqa on empty lines
-        line += '  # noqa: {0}'.format(exemptions)
-
-    # if THIS made the line too long, add an exemption for that
-    if len(line) > max_line_length and orig_len <= max_line_length:
-        line += ',E501'
-
-    return line + '\n'
-
-
-def filter_file(source, dest, output=False):
-    """Filter a single file through all the patterns in pattern_exemptions."""
-
-    # Prior to Python 3.8, `noqa: F811` needed to be placed on the `@when` line
-    # Starting with Python 3.8, it must be placed on the `def` line
-    # https://gitlab.com/pycqa/flake8/issues/583
-    ignore_f811_on_previous_line = False
-
-    with open(source) as infile:
-        parent = os.path.dirname(dest)
-        mkdirp(parent)
-
-        with open(dest, 'w') as outfile:
-            for line in infile:
-                line_errors = []
-
-                # pattern exemptions
-                for file_pattern, errors in pattern_exemptions.items():
-                    if not file_pattern.search(source):
-                        continue
-
-                    for code, patterns in errors.items():
-                        for pattern in patterns:
-                            if pattern.search(line):
-                                line_errors.append(code)
-                                break
-
-                if 'F811' in line_errors:
-                    ignore_f811_on_previous_line = True
-                elif ignore_f811_on_previous_line:
-                    line_errors.append('F811')
-                    ignore_f811_on_previous_line = False
-
-                if line_errors:
-                    line = add_pattern_exemptions(line, line_errors)
-
-                outfile.write(line)
-                if output:
-                    sys.stdout.write(line)
-
-
 def setup_parser(subparser):
     subparser.add_argument(
-        '-b', '--base', action='store', default=None,
-        help="select base branch for collecting list of modified files")
+        "-b",
+        "--base",
+        action="store",
+        default=None,
+        help="select base branch for collecting list of modified files",
+    )
     subparser.add_argument(
-        '-k', '--keep-temp', action='store_true',
-        help="do not delete temporary directory where flake8 runs. "
-             "use for debugging, to see filtered files")
+        "-a",
+        "--all",
+        action="store_true",
+        help="check all files, not just changed files",
+    )
     subparser.add_argument(
-        '-a', '--all', action='store_true',
-        help="check all files, not just changed files")
+        "-o",
+        "--output",
+        action="store_true",
+        help="send filtered files to stdout as well as temp files",
+    )
     subparser.add_argument(
-        '-o', '--output', action='store_true',
-        help="send filtered files to stdout as well as temp files")
+        "-r",
+        "--root-relative",
+        action="store_true",
+        default=False,
+        help="print root-relative paths (default: cwd-relative)",
+    )
     subparser.add_argument(
-        '-r', '--root-relative', action='store_true', default=False,
-        help="print root-relative paths (default: cwd-relative)")
+        "-U",
+        "--no-untracked",
+        dest="untracked",
+        action="store_false",
+        default=True,
+        help="exclude untracked files from checks",
+    )
     subparser.add_argument(
-        '-U', '--no-untracked', dest='untracked', action='store_false',
-        default=True, help="exclude untracked files from checks")
-    subparser.add_argument(
-        'files', nargs=argparse.REMAINDER, help="specific files to check")
+        "files", nargs=argparse.REMAINDER, help="specific files to check"
+    )
 
 
 def flake8(parser, args):
-    flake8 = which('flake8', required=True)
+    file_list = args.files
+    if file_list:
 
-    temp = tempfile.mkdtemp()
-    try:
-        file_list = args.files
-        if file_list:
-            def prefix_relative(path):
-                return os.path.relpath(
-                    os.path.abspath(os.path.realpath(path)),
-                    spack.paths.prefix)
+        def prefix_relative(path):
+            return os.path.relpath(
+                os.path.abspath(os.path.realpath(path)), spack.paths.prefix
+            )
 
-            file_list = [prefix_relative(p) for p in file_list]
+        file_list = [prefix_relative(p) for p in file_list]
 
-        with working_dir(spack.paths.prefix):
-            if not file_list:
-                file_list = changed_files(args.base, args.untracked, args.all)
+    returncode = 0
+    with working_dir(spack.paths.prefix):
+        if not file_list:
+            file_list = changed_files(args.base, args.untracked, args.all)
 
-        print('=======================================================')
-        print('flake8: running flake8 code checks on spack.')
+        print("=======================================================")
+        print("flake8: running flake8 code checks on spack.")
         print()
-        print('Modified files:')
+        print("Modified files:")
         for filename in file_list:
-            print('  {0}'.format(filename.strip()))
-        print('=======================================================')
+            print("  {0}".format(filename.strip()))
+        print("=======================================================")
 
-        # filter files into a temporary directory with exemptions added.
-        for filename in file_list:
-            src_path = os.path.join(spack.paths.prefix, filename)
-            dest_path = os.path.join(temp, filename)
-            filter_file(src_path, dest_path, args.output)
+        output = ""
+        # run in chunks of 100 at a time to avoid line length limit
+        # filename parameter in config *does not work* for this reliably
+        for chunk in grouper(file_list, 100):
+            flake8_cmd = which("flake8", required=True)
+            chunk = filter(lambda e: e is not None, chunk)
 
-        # run flake8 on the temporary tree, once for core, once for pkgs
-        package_file_list = [f for f in file_list if is_package(f)]
-        file_list         = [f for f in file_list if not is_package(f)]
+            output = flake8_cmd(
+                # use .flake8 implicitly to work around bug in flake8 upstream
+                # append-config is ignored if `--config` is explicitly listed
+                # see: https://gitlab.com/pycqa/flake8/-/issues/455
+                # "--config=.flake8",
+                *chunk,
+                fail_on_error=False,
+                output=str
+            )
+            returncode |= flake8_cmd.returncode
 
-        returncode = 0
-        with working_dir(temp):
-            output = ''
-            if file_list:
-                output += flake8(
-                    '--format', 'pylint',
-                    '--config=%s' % os.path.join(spack.paths.prefix,
-                                                 '.flake8'),
-                    *file_list, fail_on_error=False, output=str)
-                returncode |= flake8.returncode
-            if package_file_list:
-                output += flake8(
-                    '--format', 'pylint',
-                    '--config=%s' % os.path.join(spack.paths.prefix,
-                                                 '.flake8_packages'),
-                    *package_file_list, fail_on_error=False, output=str)
-                returncode |= flake8.returncode
+            if args.root_relative:
+                # print results relative to repo root.
+                print(output)
+            else:
+                # print results relative to current working directory
+                def cwd_relative(path):
+                    return "{0}: [".format(
+                        os.path.relpath(
+                            os.path.join(spack.paths.prefix, path.group(1)),
+                            os.getcwd(),
+                        )
+                    )
 
-        if args.root_relative:
-            # print results relative to repo root.
-            print(output)
-        else:
-            # print results relative to current working directory
-            def cwd_relative(path):
-                return '{0}: ['.format(os.path.relpath(
-                    os.path.join(
-                        spack.paths.prefix, path.group(1)), os.getcwd()))
+                for line in output.split("\n"):
+                    print(re.sub(r"^(.*): \[", cwd_relative, line))
 
-            for line in output.split('\n'):
-                print(re.sub(r'^(.*): \[', cwd_relative, line))
-
-        if returncode != 0:
-            print('Flake8 found errors.')
-            sys.exit(1)
-        else:
-            print('Flake8 checks were clean.')
-
-    finally:
-        if args.keep_temp:
-            print('Temporary files are in: ', temp)
-        else:
-            shutil.rmtree(temp, ignore_errors=True)
+    if returncode != 0:
+        print("Flake8 found errors.")
+        sys.exit(1)
+    else:
+        print("Flake8 checks were clean.")
diff --git a/share/spack/qa/flake8_formatter.py b/share/spack/qa/flake8_formatter.py
new file mode 100644
index 0000000000..0660a97ccf
--- /dev/null
+++ b/share/spack/qa/flake8_formatter.py
@@ -0,0 +1,146 @@
+import re
+import sys
+import pycodestyle
+from collections import defaultdict
+from flake8.formatting.default import Pylint
+from flake8.style_guide import Violation
+
+#: This is a dict that maps:
+#:  filename pattern ->
+#:     flake8 exemption code ->
+#:        list of patterns, for which matching lines should have codes applied.
+#:
+#: For each file, if the filename pattern matches, we'll add per-line
+#: exemptions if any patterns in the sub-dict match.
+pattern_exemptions = {
+    # exemptions applied only to package.py files.
+    r"package.py$": {
+        # Allow 'from spack import *' in packages, but no other wildcards
+        "F403": [
+            r"^from spack import \*$",
+            r"^from spack.pkgkit import \*$",
+        ],
+        # Exempt lines with urls and descriptions from overlong line errors.
+        "E501": [
+            r"^\s*homepage\s*=",
+            r"^\s*url\s*=",
+            r"^\s*git\s*=",
+            r"^\s*svn\s*=",
+            r"^\s*hg\s*=",
+            r"^\s*list_url\s*=",
+            r"^\s*version\(",
+            r"^\s*variant\(",
+            r"^\s*provides\(",
+            r"^\s*extends\(",
+            r"^\s*depends_on\(",
+            r"^\s*conflicts\(",
+            r"^\s*resource\(",
+            r"^\s*patch\(",
+        ],
+        # Exempt '@when' decorated functions from redefinition errors.
+        "F811": [
+            r"^\s*@when\(.*\)",
+        ],
+    },
+    # exemptions applied to all files.
+    r".py$": {
+        "E501": [
+            r"(https?|ftp|file)\:",  # URLs
+            r'([\'"])[0-9a-fA-F]{32,}\1',  # long hex checksums
+        ]
+    },
+}
+
+
+# compile all regular expressions.
+pattern_exemptions = dict(
+    (
+        re.compile(file_pattern),
+        dict(
+            (code, [re.compile(p) for p in patterns])
+            for code, patterns in error_dict.items()
+        ),
+    )
+    for file_pattern, error_dict in pattern_exemptions.items()
+)
+
+
+class SpackFormatter(Pylint):
+    def __init__(self, options):
+        self.spack_errors = {}
+        self.error_seen = False
+        super().__init__(options)
+
+    def after_init(self):  # type: () -> None
+        """Overriding to keep format string from being unset in Default"""
+        pass
+
+    def beginning(self, filename):
+        self.filename = filename
+        self.file_lines = None
+        self.spack_errors = defaultdict(list)
+        for file_pattern, errors in pattern_exemptions.items():
+            if file_pattern.search(filename):
+                for code, pat_arr in errors.items():
+                    self.spack_errors[code].extend(pat_arr)
+
+    def handle(self, error):  # type: (Violation) -> None
+        """Handle an error reported by Flake8.
+
+        This defaults to calling :meth:`format`, :meth:`show_source`, and
+        then :meth:`write`. This version implements the pattern-based ignore
+        behavior from `spack flake8` as a native flake8 plugin.
+
+        :param error:
+            This will be an instance of
+            :class:`~flake8.style_guide.Violation`.
+        :type error:
+            flake8.style_guide.Violation
+        """
+
+        # print(error.code)
+        # print(error.physical_line)
+        # get list of patterns for this error code
+        pats = self.spack_errors.get(error.code, None)
+        # if any pattern matches, skip line
+        if pats is not None and any(
+            (pat.search(error.physical_line) for pat in pats)
+        ):
+            return
+
+        # Special F811 handling
+        # Prior to Python 3.8, `noqa: F811` needed to be placed on the `@when`
+        # line
+        # Starting with Python 3.8, it must be placed on the `def` line
+        # https://gitlab.com/pycqa/flake8/issues/583
+        # we can only determine if F811 should be ignored given the previous
+        # line, so get the previous line and check it
+        if (
+            self.spack_errors.get("F811", False)
+            and error.code == "F811"
+            and error.line_number > 1
+        ):
+            if self.file_lines is None:
+                if self.filename in {"stdin", "-", "(none)", None}:
+                    self.file_lines = pycodestyle.stdin_get_value().splitlines(
+                        True
+                    )
+                else:
+                    self.file_lines = pycodestyle.readlines(self.filename)
+            for pat in self.spack_errors["F811"]:
+                if pat.search(self.file_lines[error.line_number - 2]):
+                    return
+
+        self.error_seen = True
+        line = self.format(error)
+        source = self.show_source(error)
+        self.write(line, source)
+
+    def stop(self):
+        """Override stop to check whether any errors we consider to be errors
+        were reported.
+
+        This is a hack, but it makes flake8 behave the desired way.
+        """
+        if not self.error_seen:
+            sys.exit(0)
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 0143d305ca..cbe59bc90a 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -913,7 +913,7 @@ _spack_find() {
 _spack_flake8() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -b --base -k --keep-temp -a --all -o --output -r --root-relative -U --no-untracked"
+        SPACK_COMPREPLY="-h --help -b --base -a --all -o --output -r --root-relative -U --no-untracked"
     else
         SPACK_COMPREPLY=""
     fi