feat(backends): rename MergedReadOnlyBackend to MergedSkillsBackend a… (#157)

* feat(backends): rename MergedReadOnlyBackend to MergedSkillsBackend and update documentation for clarity

refactor(paths): simplify ensure_dirs function to create only memory directory eagerly

fix(prompts): update skills availability description for accuracy

test(paths): adjust test to reflect skills directory creation on demand

* refactor(tests): format assertion for skills directory existence in ensure_dirs test

EvoScientist/EvoScientist.py

@@ -253,7 +253,7 @@ def _get_default_backend():
     """Build the default composite backend from current paths."""
     from deepagents.backends import CompositeBackend, FilesystemBackend
 
-    from .backends import CustomSandboxBackend, MergedReadOnlyBackend
+    from .backends import CustomSandboxBackend, MergedSkillsBackend
 
     workspace_dir = str(_paths_mod.WORKSPACE_ROOT)
     set_active_workspace(workspace_dir)
@@ -266,7 +266,7 @@ def _get_default_backend():
         virtual_mode=True,
         timeout=300,
     )
-    sk_backend = MergedReadOnlyBackend(
+    sk_backend = MergedSkillsBackend(
         primary_dir=user_skills_dir,
         global_dir=global_skills_dir,
         secondary_dir=SKILLS_DIR,
@@ -367,7 +367,7 @@ def create_cli_agent(workspace_dir: str | None = None, checkpointer=None, config
     from deepagents.backends import CompositeBackend, FilesystemBackend
 
     from . import paths as _paths
-    from .backends import CustomSandboxBackend, MergedReadOnlyBackend
+    from .backends import CustomSandboxBackend, MergedSkillsBackend
     from .middleware import (
         ContextOverflowMapperMiddleware,
         ToolErrorHandlerMiddleware,
@@ -407,7 +407,7 @@ def create_cli_agent(workspace_dir: str | None = None, checkpointer=None, config
         virtual_mode=True,
         timeout=300,
     )
-    sk_backend = MergedReadOnlyBackend(
+    sk_backend = MergedSkillsBackend(
         primary_dir=_usr_skills_dir,
         global_dir=_global_skills_dir,
         secondary_dir=SKILLS_DIR,

EvoScientist/backends.py

@@ -286,16 +286,17 @@ class ReadOnlyFilesystemBackend(FilesystemBackend):
         )
 
 
-class MergedReadOnlyBackend(BackendProtocol):
-    """Read-only backend that merges up to three skill directories.
+class MergedSkillsBackend(BackendProtocol):
+    """Skills backend that merges up to three skill directories.
 
     Priority (high → low):
-    1. primary   — workspace/skills/  (project-local)
-    2. global    — ~/.config/evoscientist/skills/  (user global, optional)
-    3. secondary — EvoScientist/skills/  (built-in, PyPI)
+    1. primary   — workspace/skills/  (project-local, writable)
+    2. global    — ~/.config/evoscientist/skills/  (user global, read-only)
+    3. secondary — EvoScientist/skills/  (built-in, PyPI, read-only)
 
     Higher-priority skills override lower-priority skills with the same name.
     All directories share the same virtual path namespace (/skills/).
+    Only the workspace tier (primary) allows write and edit operations.
     """
 
     def __init__(
@@ -304,9 +305,7 @@ class MergedReadOnlyBackend(BackendProtocol):
         secondary_dir: str,
         global_dir: str | None = None,
     ):
-        self._primary = ReadOnlyFilesystemBackend(
-            root_dir=primary_dir, virtual_mode=True
-        )
+        self._primary = FilesystemBackend(root_dir=primary_dir, virtual_mode=True)
         self._global = (
             ReadOnlyFilesystemBackend(root_dir=global_dir, virtual_mode=True)
             if global_dir
@@ -375,12 +374,10 @@ class MergedReadOnlyBackend(BackendProtocol):
                 pass
         return GlobResult(matches=sorted(merged.values(), key=lambda x: x["path"]))
 
-    # -- write / edit: blocked --
+    # -- write / edit: only workspace/skills/ (primary) is writable --
 
     def write(self, file_path: str, content: str) -> WriteResult:
-        return WriteResult(
-            error="This directory is read-only. Write operations are not permitted here."
-        )
+        return self._primary.write(file_path, content)
 
     def edit(
         self,
@@ -389,9 +386,7 @@ class MergedReadOnlyBackend(BackendProtocol):
         new_string: str,
         replace_all: bool = False,
     ) -> EditResult:
-        return EditResult(
-            error="This directory is read-only. Edit operations are not permitted here."
-        )
+        return self._primary.edit(file_path, old_string, new_string, replace_all)
 
     # -- download / upload --
 
@@ -410,10 +405,7 @@ class MergedReadOnlyBackend(BackendProtocol):
         return responses
 
     def upload_files(self, files: list[tuple[str, bytes]]) -> list[FileUploadResponse]:
-        return [
-            FileUploadResponse(path=path, error="permission_denied")
-            for path, _ in files
-        ]
+        return self._primary.upload_files(files)
 
 
 class CustomSandboxBackend(LocalShellBackend):

EvoScientist/paths.py

@@ -62,17 +62,15 @@ def set_workspace_root(path: str | Path) -> None:
 
 
 def ensure_dirs() -> None:
-    """Create runtime subdirectories (memory, skills) if they do not exist.
+    """Create runtime subdirectories if they do not exist.
+
+    Only memory is created eagerly — skills directories are created on demand
+    by install_skill() when the user first installs a skill.
 
     Does NOT create the workspace root itself — it should already exist
     (either the user's cwd or a directory they specified).
     """
-    for path in (MEMORY_DIR, USER_SKILLS_DIR):
-        path.mkdir(parents=True, exist_ok=True)
-    try:
-        GLOBAL_SKILLS_DIR.mkdir(parents=True, exist_ok=True)
-    except PermissionError:
-        pass  # read-only environments — skip silently
+    MEMORY_DIR.mkdir(parents=True, exist_ok=True)
 
 
 def default_workspace_dir() -> Path:

EvoScientist/prompts.py

@@ -15,7 +15,7 @@ into reproducible experiments and a paper-ready experimental report.
 - Never invent results. If you cannot run something, say so and propose the smallest next step.
 - Delegate aggressively using the `task` tool. Prefer the research sub-agent for web search.
 - Use local skills when they match the task. Your available skills are listed in the system prompt — read the relevant `SKILL.md` for full instructions.
-  All skills are available under `/skills/` (read-only).
+  All skills are available under `/skills/`.
 
 ## Research Lifecycle (when applicable)
 For end-to-end research projects, the recommended skill sequence is:

tests/test_paths.py

@@ -102,4 +102,6 @@ class TestEnsureDirsUsesUpdatedPaths:
         paths.ensure_dirs()
 
         assert (new_root / "memory").is_dir()
-        assert (new_root / "skills").is_dir()
+        assert not (
+            new_root / "skills"
+        ).exists()  # skills created on demand by install_skill()