diff --git a/pre_commit/clientlib.py b/pre_commit/clientlib.py
index da6ca2be..11e02864 100644
--- a/pre_commit/clientlib.py
+++ b/pre_commit/clientlib.py
@@ -81,6 +81,7 @@ MANIFEST_HOOK_DICT = cfgv.Map(
     cfgv.Optional('require_serial', cfgv.check_bool, False),
     cfgv.Optional('stages', cfgv.check_array(cfgv.check_one_of(C.STAGES)), []),
     cfgv.Optional('verbose', cfgv.check_bool, False),
+    cfgv.Optional('run_all', cfgv.check_bool, True),
 )
 MANIFEST_SCHEMA = cfgv.Array(MANIFEST_HOOK_DICT)
 
diff --git a/pre_commit/commands/run.py b/pre_commit/commands/run.py
index 429e04c6..6a22ab93 100644
--- a/pre_commit/commands/run.py
+++ b/pre_commit/commands/run.py
@@ -126,9 +126,11 @@ class Classifier:
         return Classifier(filenames)
 
 
-def _get_skips(environ: MutableMapping[str, str]) -> set[str]:
+def _get_skips(environ: MutableMapping[str, str], args: argparse.Namespace, hooks: list[Hook]) -> set[str]:
     skips = environ.get('SKIP', '')
-    return {skip.strip() for skip in skips.split(',') if skip.strip()}
+    environ_skips = {skip.strip() for skip in skips.split(',') if skip.strip()}
+    context_skips = {h.id for h in hooks if args.all_files and not h.run_all}
+    return environ_skips | context_skips
 
 
 SKIPPED = 'Skipped'
@@ -419,7 +421,7 @@ def run(
             )
             return 1
 
-        skips = _get_skips(environ)
+        skips = _get_skips(environ, args, hooks)
         to_install = [
             hook
             for hook in hooks
diff --git a/pre_commit/hook.py b/pre_commit/hook.py
index 202abb35..36473672 100644
--- a/pre_commit/hook.py
+++ b/pre_commit/hook.py
@@ -36,6 +36,7 @@ class Hook(NamedTuple):
     require_serial: bool
     stages: Sequence[str]
     verbose: bool
+    run_all: bool
 
     @property
     def cmd(self) -> tuple[str, ...]: