diff --git a/examples/filereference/inputs.json b/examples/filereference/inputs.json
deleted file mode 100644
index e2626cec..00000000
--- a/examples/filereference/inputs.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
-  "inputs": {
-    "data": [
-      "sample_0.json",
-      "sample_1.json",
-      "sample_2.json",
-      "sample_3.json",
-      "sample_4.json",
-      "sample_5.json",
-      "sample_6.json",
-      "sample_7.json",
-      "sample_8.json",
-      "sample_9.json"
-    ]
-  }
-}
diff --git a/examples/filereference/tesseract_api.py b/examples/filereference/tesseract_api.py
deleted file mode 100644
index fef9584e..00000000
--- a/examples/filereference/tesseract_api.py
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 2025 Pasteur Labs. All Rights Reserved.
-# SPDX-License-Identifier: Apache-2.0
-
-import shutil
-from pathlib import Path
-
-from pydantic import BaseModel
-
-from tesseract_core.runtime.config import get_config
-from tesseract_core.runtime.experimental import (
-    InputFileReference,
-    OutputFileReference,
-)
-
-
-class InputSchema(BaseModel):
-    data: list[InputFileReference]
-
-
-class OutputSchema(BaseModel):
-    data: list[OutputFileReference]
-
-
-def apply(inputs: InputSchema) -> OutputSchema:
-    output_path = Path(get_config().output_path)
-    files = []
-    for source in inputs.data:
-        # source is a pathlib.Path starting with /path/to/input_path/...
-        target = output_path / source.name
-        # target must be a pathlib.Path at /path/to/output_path
-        target = target.with_suffix(".copy")
-        shutil.copy(source, target)
-        files.append(target)
-    return OutputSchema(data=files)
diff --git a/examples/filereference/tesseract_config.yaml b/examples/filereference/tesseract_config.yaml
deleted file mode 100644
index 92219a45..00000000
--- a/examples/filereference/tesseract_config.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-name: filereference
-version: "1.0.0"
-description: |
-  Tesseract that loads data from a folder.
-
-build_config:
-  package_data: []
-  custom_build_steps: []
diff --git a/examples/filereference/test_tesseract.py b/examples/filereference/test_tesseract.py
deleted file mode 100644
index b8ca5af2..00000000
--- a/examples/filereference/test_tesseract.py
+++ /dev/null
@@ -1,40 +0,0 @@
-from pathlib import Path
-
-from rich import print
-
-from tesseract_core import Tesseract
-
-here = Path(__file__).parent.resolve()
-input_path = Path("./testdata")
-output_path = Path("./output")
-
-# these are relative to input_path
-data = [
-    "sample_0.json",
-    "sample_1.json",
-    "sample_2.json",
-    "sample_3.json",
-    "sample_4.json",
-    "sample_5.json",
-    "sample_6.json",
-    "sample_7.json",
-    "sample_8.json",
-    "sample_9.json",
-]
-
-with Tesseract.from_tesseract_api(
-    "tesseract_api.py", input_path=input_path, output_path=output_path
-) as tess:
-    result = tess.apply({"data": data})
-    print(result)
-    assert all((output_path / p).exists() for p in result["data"])
-
-
-with Tesseract.from_image(
-    "filereference",
-    input_path=input_path,
-    output_path=output_path,
-) as tess:
-    result = tess.apply({"data": data})
-    print(result)
-    assert all((output_path / p).exists() for p in result["data"])
diff --git a/examples/filereference/.gitignore b/examples/pathreference/.gitignore
similarity index 100%
rename from examples/filereference/.gitignore
rename to examples/pathreference/.gitignore
diff --git a/examples/pathreference/README.md b/examples/pathreference/README.md
new file mode 100644
index 00000000..5218da4c
--- /dev/null
+++ b/examples/pathreference/README.md
@@ -0,0 +1,101 @@
+# Path Reference Example
+
+A Tesseract that copies files and directories from `input_path` to `output_path`.
+It demonstrates how to use `Path` in Tesseract schemas and how to compose custom
+Pydantic validators on top of the built-in path-handling behaviour.
+
+## What `Path` does in a schema
+
+When you annotate a field with `Path`, the schema generation layer automatically
+injects path-handling validators at runtime.
+
+**Input `Path` fields** — caller sends a relative string, `apply` receives an absolute `Path`:
+
+```
+caller sends       →  "sample_8.json"
+built-in resolves  →  Path("/tesseract/input_data/sample_8.json")   (checked: exists)
+apply sees         →  Path("/tesseract/input_data/sample_8.json")
+```
+
+- Rejects any path that would escape `input_path` (path traversal protection).
+- Raises `FileNotFoundError` if the resolved path does not exist.
+- Accepts both files **and** directories (use `InputFileReference` for files only).
+
+**Output `Path` fields** — `apply` returns an absolute `Path`, caller receives a relative string:
+
+```
+apply returns      →  Path("/tesseract/output_data/sample_8.copy")
+built-in strips    →  Path("sample_8.copy")                          (checked: exists)
+caller receives    →  "sample_8.copy"
+```
+
+- Raises `ValueError` if the path does not exist inside `output_path`.
+- Accepts both files **and** directories (use `OutputFileReference` for files only).
+
+## Composing user-defined validators
+
+`AfterValidator`s placed on a `Path`-annotated field are preserved, and in both
+cases the user validator receives an already-resolved **absolute** `Path`:
+
+```python
+def has_bin_sidecar(path: Path) -> Path:
+    """Check that any binref JSON has its .bin sidecar present."""
+    if path.is_file():
+        name = bin_reference(path)
+        if name is not None:
+            bin = path.parent / name
+            assert bin.exists(), f"Expected .bin file for json {path} not found at {bin}"
+    else:
+        raise ValueError(f"{path} does not exist or is not a file.")
+    return path
+
+class InputSchema(BaseModel):
+    paths: list[Annotated[Path, AfterValidator(has_bin_sidecar)]]
+```
+
+The built-in path validators run at different points depending on direction:
+
+**Input fields** — built-in validator runs **first**, user validators run after:
+
+```
+"sample_8.json"
+  → built-in         →  Path("/tesseract/input_data/sample_8.json")   (resolved + existence check)
+  → has_bin_sidecar  →  Path("/tesseract/input_data/sample_8.json")   (checks .bin sidecar present)
+  → apply receives   →  Path("/tesseract/input_data/sample_8.json")
+```
+
+**Output fields** — user validators run **first**, built-in validator runs after:
+
+```
+apply returns  →  Path("/tesseract/output_data/sample_8.copy")
+  → has_bin_sidecar  →  Path("/tesseract/output_data/sample_8.copy")   (checks .bin sidecar was copied)
+  → built-in         →  Path("sample_8.copy")                          (existence check + prefix stripped)
+  → caller receives  →  "sample_8.copy"
+```
+
+This example uses output validators to confirm that `apply` copied the sidecar
+`.bin` file alongside each JSON file.
+
+## Test data
+
+The test dataset (`test_cases/testdata/`) contains:
+
+| File                                                               | Array encoding                                  |
+| ------------------------------------------------------------------ | ----------------------------------------------- |
+| `sample_0.json`, `sample_3.json`, `sample_6.json`, `sample_9.json` | `json` (inline)                                 |
+| `sample_1.json`, `sample_4.json`, `sample_7.json`                  | `base64` (inline)                               |
+| `sample_2.json`, `sample_5.json`, `sample_8.json`                  | `binref` (references the shared `.bin` sidecar) |
+| `sample_dir/`                                                      | directory containing `data.json`                |
+
+`generate_data.py` re-creates this dataset using a fixed RNG seed.
+
+## Running
+
+```bash
+# local (no Docker)
+uv run python test_tesseract.py
+
+# build Docker image first, then re-run
+uv run tesseract build .
+uv run python test_tesseract.py
+```
diff --git a/examples/filereference/generate_data.py b/examples/pathreference/generate_data.py
similarity index 100%
rename from examples/filereference/generate_data.py
rename to examples/pathreference/generate_data.py
diff --git a/examples/pathreference/tesseract_api.py b/examples/pathreference/tesseract_api.py
new file mode 100644
index 00000000..3d724192
--- /dev/null
+++ b/examples/pathreference/tesseract_api.py
@@ -0,0 +1,64 @@
+# Copyright 2025 Pasteur Labs. All Rights Reserved.
+# SPDX-License-Identifier: Apache-2.0
+
+import json
+import shutil
+from pathlib import Path
+from typing import Annotated
+
+from pydantic import AfterValidator, BaseModel
+
+from tesseract_core.runtime.config import get_config
+
+
+def bin_reference(path: Path) -> str | None:
+    """Return the name of the .bin file if the json at 'path' references one, else None."""
+    with open(path) as f:
+        contents = json.load(f)
+        if contents["data"]["encoding"] == "binref":
+            return contents["data"]["buffer"].split(":")[0]
+    return None
+
+
+def has_bin_sidecar(path: Path) -> Path:
+    """Pydantic validator to check for .bin file next to any json file that references one."""
+    if path.is_file():
+        name = bin_reference(path)
+        if name is not None:
+            bin = path.parent / name
+            assert bin.exists(), (
+                f"Expected .bin file for json {json} not found at {bin}"
+            )
+    elif path.is_dir():
+        return path
+    else:
+        raise ValueError(f"{path} does not exist.")
+    return path
+
+
+class InputSchema(BaseModel):
+    paths: list[Annotated[Path, AfterValidator(has_bin_sidecar)]]
+
+
+class OutputSchema(BaseModel):
+    paths: list[Annotated[Path, AfterValidator(has_bin_sidecar)]]
+
+
+def apply(inputs: InputSchema) -> OutputSchema:
+    output_path = Path(get_config().output_path)
+    result = []
+
+    for src in inputs.paths:
+        if src.is_dir():
+            # copy any folder that is given
+            dest = output_path / src.name
+            shutil.copytree(src, dest)
+        else:
+            # copy any file that is given, and if it references a .bin file, copy that too
+            dest = output_path / src.with_suffix(".copy").name
+            shutil.copy(src, dest)
+            bin = bin_reference(src)
+            if bin is not None:
+                shutil.copy(src.parent / bin, dest.parent / bin)
+        result.append(dest)
+    return OutputSchema(paths=result)
diff --git a/examples/pathreference/tesseract_config.yaml b/examples/pathreference/tesseract_config.yaml
new file mode 100644
index 00000000..ca1245aa
--- /dev/null
+++ b/examples/pathreference/tesseract_config.yaml
@@ -0,0 +1,10 @@
+name: pathreference
+version: "1.0.0"
+description: |
+  Tesseract that copies input files and directories to the output directory.
+  Demonstrates InputPathReference and OutputPathReference, which accept both
+  files and directories.
+
+build_config:
+  package_data: []
+  custom_build_steps: []
diff --git a/examples/filereference/test_cases/test_apply.json b/examples/pathreference/test_cases/test_apply.json
similarity index 85%
rename from examples/filereference/test_cases/test_apply.json
rename to examples/pathreference/test_cases/test_apply.json
index 13208964..058c4e64 100644
--- a/examples/filereference/test_cases/test_apply.json
+++ b/examples/pathreference/test_cases/test_apply.json
@@ -1,7 +1,7 @@
 {
   "endpoint": "apply",
   "expected_outputs": {
-    "data": [
+    "paths": [
       "sample_0.copy",
       "sample_1.copy",
       "sample_2.copy",
@@ -11,7 +11,8 @@
       "sample_6.copy",
       "sample_7.copy",
       "sample_8.copy",
-      "sample_9.copy"
+      "sample_9.copy",
+      "sample_dir"
     ]
   },
   "expected_exception": null,
@@ -23,7 +24,7 @@
   },
   "payload": {
     "inputs": {
-      "data": [
+      "paths": [
         "sample_0.json",
         "sample_1.json",
         "sample_2.json",
@@ -33,7 +34,8 @@
         "sample_6.json",
         "sample_7.json",
         "sample_8.json",
-        "sample_9.json"
+        "sample_9.json",
+        "sample_dir"
       ]
     }
   }
diff --git a/examples/filereference/test_cases/testdata/a2af4236-15c5-40ec-9014-b79f9cbad50c.bin b/examples/pathreference/test_cases/testdata/a2af4236-15c5-40ec-9014-b79f9cbad50c.bin
similarity index 100%
rename from examples/filereference/test_cases/testdata/a2af4236-15c5-40ec-9014-b79f9cbad50c.bin
rename to examples/pathreference/test_cases/testdata/a2af4236-15c5-40ec-9014-b79f9cbad50c.bin
diff --git a/examples/filereference/test_cases/testdata/sample_0.json b/examples/pathreference/test_cases/testdata/sample_0.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_0.json
rename to examples/pathreference/test_cases/testdata/sample_0.json
diff --git a/examples/filereference/test_cases/testdata/sample_1.json b/examples/pathreference/test_cases/testdata/sample_1.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_1.json
rename to examples/pathreference/test_cases/testdata/sample_1.json
diff --git a/examples/filereference/test_cases/testdata/sample_2.json b/examples/pathreference/test_cases/testdata/sample_2.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_2.json
rename to examples/pathreference/test_cases/testdata/sample_2.json
diff --git a/examples/filereference/test_cases/testdata/sample_3.json b/examples/pathreference/test_cases/testdata/sample_3.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_3.json
rename to examples/pathreference/test_cases/testdata/sample_3.json
diff --git a/examples/filereference/test_cases/testdata/sample_4.json b/examples/pathreference/test_cases/testdata/sample_4.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_4.json
rename to examples/pathreference/test_cases/testdata/sample_4.json
diff --git a/examples/filereference/test_cases/testdata/sample_5.json b/examples/pathreference/test_cases/testdata/sample_5.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_5.json
rename to examples/pathreference/test_cases/testdata/sample_5.json
diff --git a/examples/filereference/test_cases/testdata/sample_6.json b/examples/pathreference/test_cases/testdata/sample_6.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_6.json
rename to examples/pathreference/test_cases/testdata/sample_6.json
diff --git a/examples/filereference/test_cases/testdata/sample_7.json b/examples/pathreference/test_cases/testdata/sample_7.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_7.json
rename to examples/pathreference/test_cases/testdata/sample_7.json
diff --git a/examples/filereference/test_cases/testdata/sample_8.json b/examples/pathreference/test_cases/testdata/sample_8.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_8.json
rename to examples/pathreference/test_cases/testdata/sample_8.json
diff --git a/examples/filereference/test_cases/testdata/sample_9.json b/examples/pathreference/test_cases/testdata/sample_9.json
similarity index 100%
rename from examples/filereference/test_cases/testdata/sample_9.json
rename to examples/pathreference/test_cases/testdata/sample_9.json
diff --git a/examples/pathreference/test_cases/testdata/sample_dir/data.json b/examples/pathreference/test_cases/testdata/sample_dir/data.json
new file mode 100644
index 00000000..39adceba
--- /dev/null
+++ b/examples/pathreference/test_cases/testdata/sample_dir/data.json
@@ -0,0 +1 @@
+{ "value": "world" }
diff --git a/examples/pathreference/test_tesseract.py b/examples/pathreference/test_tesseract.py
new file mode 100644
index 00000000..7d265937
--- /dev/null
+++ b/examples/pathreference/test_tesseract.py
@@ -0,0 +1,47 @@
+import shutil
+from pathlib import Path
+
+from rich import print
+
+from tesseract_core import Tesseract
+
+
+def clean():
+    # delete before copy
+    if output_path.exists():
+        shutil.rmtree(output_path)
+    output_path.mkdir()
+
+
+input_path = Path("./test_cases/testdata")
+output_path = Path("./output")
+
+# mix of a file and a directory, both relative to input_path
+paths = [
+    "sample_0.json",
+    "sample_8.json",  # contains .bin reference
+    "sample_dir",
+]
+
+clean()
+with Tesseract.from_tesseract_api(
+    "tesseract_api.py", input_path=input_path, output_path=output_path, stream_logs=True
+) as tess:
+    result = tess.apply({"paths": paths})
+    print(result)
+    out_paths = [(output_path / p) for p in result["paths"]]
+    assert len(out_paths) == len(paths)
+    assert all(p.exists() for p in out_paths)
+    assert len(list(output_path.glob("*.bin"))) == 1
+
+
+clean()
+with Tesseract.from_image(
+    "pathreference", input_path=input_path, output_path=output_path, stream_logs=True
+) as tess:
+    result = tess.apply({"paths": paths})
+    print(result)
+    out_paths = [(output_path / p) for p in result["paths"]]
+    assert len(out_paths) == len(paths)
+    assert all(p.exists() for p in out_paths)
+    assert len(list(output_path.glob("*.bin"))) == 1
diff --git a/tesseract_core/runtime/experimental.py b/tesseract_core/runtime/experimental.py
index 4b7013a3..b5f1c536 100644
--- a/tesseract_core/runtime/experimental.py
+++ b/tesseract_core/runtime/experimental.py
@@ -20,6 +20,7 @@
 from pydantic.json_schema import JsonSchemaValue
 from pydantic_core import CoreSchema, SchemaSerializer, SchemaValidator, core_schema
 
+from tesseract_core.runtime.config import get_config
 from tesseract_core.runtime.file_interactions import PathLike, parent_path
 from tesseract_core.runtime.gradient_endpoint_derivation import (
     jacobian_from_jvp,
@@ -226,6 +227,11 @@ def _resolve_input_path(path: Path) -> Path:
         )
     if not tess_path.exists():
         raise FileNotFoundError(f"Input path {tess_path} does not exist.")
+    return tess_path
+
+
+def _resolve_input_file(path: Path) -> Path:
+    tess_path = _resolve_input_path(path)
     if not tess_path.is_file():
         raise ValueError(f"Input path {tess_path} is not a file.")
     return tess_path
@@ -241,8 +247,16 @@ def _strip_output_path(path: Path) -> Path:
         return path
 
 
-InputFileReference = Annotated[Path, AfterValidator(_resolve_input_path)]
-OutputFileReference = Annotated[Path, AfterValidator(_strip_output_path)]
+def _strip_output_file(path: Path) -> Path:
+    stripped = _strip_output_path(path)
+    full_path = Path(get_config().output_path) / stripped
+    if not full_path.is_file():
+        raise ValueError(f"Output path {full_path} is not a file.")
+    return stripped
+
+
+InputFileReference = Annotated[Path, AfterValidator(_resolve_input_file)]
+OutputFileReference = Annotated[Path, AfterValidator(_strip_output_file)]
 
 
 def require_file(file_path: PathLike) -> Path:
diff --git a/tesseract_core/runtime/schema_generation.py b/tesseract_core/runtime/schema_generation.py
index dad8d2e0..07b906d7 100644
--- a/tesseract_core/runtime/schema_generation.py
+++ b/tesseract_core/runtime/schema_generation.py
@@ -5,6 +5,7 @@
 import types
 from collections.abc import Callable, Iterable, Mapping, Sequence
 from copy import copy
+from pathlib import Path
 from typing import (
     Annotated,
     Any,
@@ -42,6 +43,69 @@
 SEQ_INDEX_SENTINEL = object()
 DICT_INDEX_SENTINEL = object()
 
+
+def _resolve_input_path(path: Path) -> Path:
+    from tesseract_core.runtime.config import get_config
+
+    input_path = get_config().input_path
+    tess_path = (input_path / path).resolve()
+    if str(input_path) not in str(tess_path):
+        raise ValueError(
+            f"Invalid input file reference: {path}. "
+            f"Expected path to be relative to {input_path}, but got {tess_path}. "
+            "File references have to be relative to --input-path."
+        )
+    if not tess_path.exists():
+        raise FileNotFoundError(f"Input path {tess_path} does not exist.")
+    return tess_path
+
+
+def _strip_output_path(path: Path) -> Path:
+    from tesseract_core.runtime.config import get_config
+
+    output_path = get_config().output_path
+    if path.is_relative_to(output_path):
+        return path.relative_to(output_path)
+    else:
+        return path
+
+
+def _strip_output_exists(path: Path) -> Path:
+    from tesseract_core.runtime.config import get_config
+
+    stripped = _strip_output_path(path)
+    full_path = Path(get_config().output_path) / stripped
+    if not full_path.exists():
+        raise ValueError(f"Output path {full_path} does not exist.")
+    return stripped
+
+
+def _is_annotated_path(x: Any) -> bool:
+    def _core_type(ttype: Any) -> Any:
+        while _is_annotated(ttype):
+            ttype = ttype.__origin__
+        return ttype
+
+    return _is_annotated(x) and _core_type(x) is Path
+
+
+def _inject_input_path_validator(x: Any, _: tuple) -> Any:
+    if x is Path:
+        # Wrap with _resolve_input_path as the INNERMOST validator so that
+        # it runs before all user validators (if any)
+        return Annotated[Path, AfterValidator(_resolve_input_path)]
+    return x
+
+
+def _inject_output_path_validator(x: Any, _: Any) -> Any:
+    if x is not Path and not _is_annotated_path(x):
+        return x
+    # x is either bare Path or Annotated[Path, *user_validators]
+    # Wrap with _strip_output_exists as the OUTERMOST validator so user validators
+    # run first (on absolute paths) and stripping happens last.
+    return Annotated[x, AfterValidator(_strip_output_exists)]
+
+
 T = TypeVar("T")
 
 # Python has funnily enough two union types now. See https://github.com/python/cpython/issues/105499
@@ -68,6 +132,7 @@ def apply_function_to_model_tree(
     func: Callable[[type, tuple], type],
     model_prefix: str = "",
     default_model_config: dict[str, Any] | None = None,
+    is_leaf: Callable[[Any], bool] | None = None,
 ) -> type[BaseModel]:
     """Apply a function to all leaves of a Pydantic model, recursing into containers + nested models.
 
@@ -85,6 +150,11 @@ class MyModel(BaseModel):
 
     The path to the field "a" would be ["a"], and the path to the int type would be
     ["a", SEQ_INDEX_SENTINEL, DICT_INDEX_SENTINEL].
+
+    The optional ``is_leaf`` predicate, if provided, is checked first: when it returns
+    True for a node, ``func`` is called on that node immediately without further recursion.
+    This allows callers to treat compound types (e.g. ``Annotated[Path, ...]``) as atomic
+    leaves.
     """
     if default_model_config is None:
         default_model_config = {}
@@ -92,6 +162,10 @@ class MyModel(BaseModel):
     seen_models = set()
 
     def _recurse_over_model_tree(treeobj: Any, path: list[str]) -> Any:
+        # If the caller says this node is a leaf, apply func immediately
+        if is_leaf is not None and is_leaf(treeobj):
+            return func(treeobj, tuple(path))
+
         # Get the origin type of the annotation, e.g. List for List[int]
         origin_type = get_origin(treeobj)
         deprecated_types = ["List", "Dict", "Set", "FrozenSet", "Tuple"]
@@ -268,15 +342,17 @@ def create_apply_schema(
 
     InputSchema = apply_function_to_model_tree(
         InputSchema,
-        lambda x, _: x,
+        _inject_input_path_validator,
         model_prefix="Apply_",
         default_model_config=dict(extra="forbid"),
     )
+
     OutputSchema = apply_function_to_model_tree(
         OutputSchema,
-        lambda x, _: x,
+        _inject_output_path_validator,
         model_prefix="Apply_",
         default_model_config=dict(extra="forbid"),
+        is_leaf=_is_annotated_path,
     )
 
     class ApplyInputSchema(BaseModel):
diff --git a/tests/endtoend_tests/test_examples.py b/tests/endtoend_tests/test_examples.py
index c8db19a4..df3351f0 100644
--- a/tests/endtoend_tests/test_examples.py
+++ b/tests/endtoend_tests/test_examples.py
@@ -102,7 +102,7 @@ class Config:
     "fortran_heat": Config(),
     "conda": Config(),
     "required_files": Config(input_path="input"),
-    "filereference": Config(input_path="test_cases/testdata", output_path="output"),
+    "pathreference": Config(input_path="test_cases/testdata", output_path="output"),
     "metrics": Config(test_with_random_inputs=True),
     "qp_solve": Config(),
     "tesseractreference": Config(),  # Can't test requests standalone; needs target Tesseract. Covered in separate test.
diff --git a/tests/runtime_tests/test_schema_generation.py b/tests/runtime_tests/test_schema_generation.py
index 8fd04579..3011bebe 100644
--- a/tests/runtime_tests/test_schema_generation.py
+++ b/tests/runtime_tests/test_schema_generation.py
@@ -4,11 +4,12 @@
 import json
 from collections.abc import Iterable
 from copy import deepcopy
+from pathlib import Path
 from typing import Annotated, Optional
 
 import numpy as np
 import pytest
-from pydantic import BaseModel, ConfigDict, RootModel, ValidationError
+from pydantic import AfterValidator, BaseModel, ConfigDict, RootModel, ValidationError
 
 from tesseract_core.runtime import Array, Differentiable, Float32, Float64, Int64, UInt8
 from tesseract_core.runtime.experimental import LazySequence
@@ -809,3 +810,226 @@ class Parent(BaseModel):
 
     with pytest.raises(ValidationError):
         ApplyParent.model_validate({"child": {"x": "foo"}, "extra": 1})
+
+
+# =============================================================================
+# Path resolution tests (automatic path handling in Input/OutputSchema)
+# =============================================================================
+
+
+@pytest.fixture
+def runtime_config(tmp_path):
+    """Fixture providing a real RuntimeConfig with temp input/output dirs.
+
+    Patches get_config() so that path-resolution validators use these dirs.
+    Restores the original config state on teardown.
+    """
+    import tesseract_core.runtime.config as _cfg_mod
+    from tesseract_core.runtime.config import get_config, update_config
+
+    original_config = _cfg_mod._current_config
+    original_overrides = _cfg_mod._config_overrides.copy()
+
+    input_dir = tmp_path / "inputs"
+    output_dir = tmp_path / "outputs"
+    input_dir.mkdir()
+    output_dir.mkdir()
+
+    update_config(input_path=str(input_dir), output_path=str(output_dir))
+    yield get_config()
+
+    _cfg_mod._current_config = original_config
+    _cfg_mod._config_overrides = original_overrides
+
+
+# --- Input: basic resolution ---
+
+
+def test_input_relative_path_resolved_to_absolute(runtime_config):
+    """Caller sends relative string → apply() receives absolute Path under input_path."""
+    input_path = Path(runtime_config.input_path)
+    (input_path / "data.txt").touch()
+    (input_path / "mydir").mkdir()
+
+    class InputSchema(BaseModel):
+        file: Path
+        folder: Path
+
+    ApplyInput, _ = create_apply_schema(InputSchema, InputSchema)
+    result = ApplyInput.model_validate(
+        {"inputs": {"file": "data.txt", "folder": "mydir"}}
+    )
+    assert result.inputs.file == input_path / "data.txt"
+    assert result.inputs.file.is_absolute()
+
+
+@pytest.mark.parametrize(
+    "path,exc,match",
+    [
+        ("missing.txt", FileNotFoundError, "does not exist"),
+        ("../../etc/passwd", ValidationError, "relative to"),
+    ],
+)
+def test_input_invalid_path_raises(runtime_config, path, exc, match):
+    class InputSchema(BaseModel):
+        file: Path
+
+    ApplyInput, _ = create_apply_schema(InputSchema, InputSchema)
+    with pytest.raises(exc, match=match):
+        ApplyInput.model_validate({"inputs": {"file": path}})
+
+
+# --- Input: container and optional types ---
+
+
+def test_input_list_of_paths_all_resolved(runtime_config):
+    """list[Path] — every entry is resolved to an absolute path."""
+    input_path = Path(runtime_config.input_path)
+    (input_path / "a.txt").touch()
+    (input_path / "b.txt").touch()
+
+    class InputSchema(BaseModel):
+        files: list[Path]
+        non_path_field: int
+
+    ApplyInput, _ = create_apply_schema(InputSchema, InputSchema)
+    result = ApplyInput.model_validate(
+        {"inputs": {"files": ["a.txt", "b.txt"], "non_path_field": 1}}
+    )
+    assert result.inputs.files == [input_path / "a.txt", input_path / "b.txt"]
+
+
+def test_input_optional_path(runtime_config):
+    input_path = Path(runtime_config.input_path)
+
+    class InputSchema(BaseModel):
+        file: Path | None = None
+
+    # None works
+    ApplyInput, _ = create_apply_schema(InputSchema, InputSchema)
+    result = ApplyInput.model_validate({"inputs": {"file": None}})
+    assert result.inputs.file is None
+
+    # Path as well
+    (input_path / "data.txt").touch()
+    ApplyInput, _ = create_apply_schema(InputSchema, InputSchema)
+    result = ApplyInput.model_validate({"inputs": {"file": "data.txt"}})
+    assert result.inputs.file == input_path / "data.txt"
+
+
+# --- Input: user validators ---
+
+
+def test_input_user_validator_receives_absolute_path(runtime_config):
+    """AfterValidator on an input Path field receives the already-resolved absolute path.
+
+    From the README:
+        "sample_8.json"
+          → built-in resolves → Path("/tesseract/input_data/sample_8.json")
+          → user validator   → Path("/tesseract/input_data/sample_8.json")
+    """
+    input_path = Path(runtime_config.input_path)
+    (input_path / "data.txt").touch()
+
+    seen: list[Path] = []
+
+    def record(path: Path) -> Path:
+        seen.append(path)
+        return path
+
+    class InputSchema(BaseModel):
+        file: Annotated[Path, AfterValidator(record)]
+
+    ApplyInput, _ = create_apply_schema(InputSchema, InputSchema)
+    ApplyInput.model_validate({"inputs": {"file": "data.txt"}})
+
+    assert len(seen) == 1
+    assert seen[0] == input_path / "data.txt"
+    assert seen[0].is_absolute()
+
+
+# --- Output: basic stripping ---
+
+
+def test_output_absolute_path_stripped_to_relative(runtime_config):
+    """apply() returns absolute Path → caller receives relative Path.
+
+    From the README:
+        apply returns  →  Path("/tesseract/output_data/sample_8.copy")
+        built-in strips → Path("sample_8.copy")
+        caller receives → "sample_8.copy"
+    """
+    output_path = Path(runtime_config.output_path)
+    (output_path / "result.txt").touch()
+
+    class OutputSchema(BaseModel):
+        result: Path
+
+    _, ApplyOutput = create_apply_schema(OutputSchema, OutputSchema)
+    out = ApplyOutput.model_validate({"result": output_path / "result.txt"})
+    assert out.root.result == Path("result.txt")
+    assert not out.root.result.is_absolute()
+
+
+def test_output_nonexistent_path_raises(runtime_config):
+    """ValueError when the output path does not exist."""
+    output_path = Path(runtime_config.output_path)
+
+    class OutputSchema(BaseModel):
+        result: Path
+
+    _, ApplyOutput = create_apply_schema(OutputSchema, OutputSchema)
+    with pytest.raises(ValidationError, match="does not exist"):
+        ApplyOutput.model_validate({"result": output_path / "ghost.txt"})
+
+
+def test_output_list_of_paths_all_stripped(runtime_config):
+    """list[Path] — all output paths stripped to relative."""
+    output_path = Path(runtime_config.output_path)
+    (output_path / "a.out").touch()
+    (output_path / "b.out").touch()
+
+    class OutputSchema(BaseModel):
+        files: list[Path]
+        other_non_path_field: int
+
+    _, ApplyOutput = create_apply_schema(OutputSchema, OutputSchema)
+    out = ApplyOutput.model_validate(
+        {
+            "files": [output_path / "a.out", output_path / "b.out"],
+            "other_non_path_field": 1,
+        }
+    )
+    assert out.root.files == [Path("a.out"), Path("b.out")]
+
+
+# --- Output: user validators ---
+
+
+def test_output_user_validator_receives_absolute_path(runtime_config):
+    """AfterValidator on an output Path field receives the absolute path before stripping.
+
+    From the README:
+        apply returns    → Path("/tesseract/output_data/sample_8.copy")
+          → user validator → Path("/tesseract/output_data/sample_8.copy")  ← absolute
+          → built-in       → Path("sample_8.copy")                          ← stripped
+    """
+    output_path = Path(runtime_config.output_path)
+    output_file = output_path / "result.txt"
+    output_file.touch()
+
+    seen: list[Path] = []
+
+    def record(path: Path) -> Path:
+        seen.append(path)
+        return path
+
+    class OutputSchema(BaseModel):
+        result: Annotated[Path, AfterValidator(record)]
+
+    _, ApplyOutput = create_apply_schema(OutputSchema, OutputSchema)
+    out = ApplyOutput.model_validate({"result": output_file})
+
+    assert len(seen) == 1
+    assert seen[0] == output_file  # absolute, not yet stripped
+    assert out.root.result == Path("result.txt")  # final result is stripped