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refactor(tools): move the filesystem tools into tinytools-std behind an FsGate seam - #6804
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Remove the entire set of legacy filesystem tool implementations and their tests, including apply_patch, csv_export, edit_file, file_read, file_write, git_operations, glob_search, grep, list_files, read_diff, run_linter, run_tests, update_memory_md, and write_sink. These tools have been replaced by a new consolidated implementation, and keeping the old code would cause confusion and maintenance burden. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
The filesystem and shell tool implementations now properly produce output artifacts when they create or modify files, ensuring that downstream middleware can track and process these artifacts. This change adds artifact generation to the filesystem write operations and shell command execution, aligning their behavior with the existing artifact handling infrastructure. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
The domain family test was using an invalid domain format that did not match the expected input pattern, causing the test to fail. Updated the test to use a properly formatted domain string that aligns with the validation logic in the ops module. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
The import of `ToolRunContext` from `tinytools` was moved after the `tinyagents_harness` imports to follow the project's import ordering conventions, ensuring consistency across the codebase without changing any behavior. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
Add fs2, glob, libc, regex, and walkdir to the dependency list in Cargo.lock to support upcoming file system operations and pattern matching functionality. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
…ter role The filesystem tools table entry now explains that the tools themselves live in `tinytools_std::filesystem` and are imported directly, while only the `SecurityPolicy` gate is implemented in the host adapter, making the architecture clearer. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
Updates the README files in the tools directory to reflect that the built-in filesystem tools now live in the vendored `tinytools` crate, with the local directory containing only the `FsGate` security policy adapter. Also documents the parallel security context implementations in `system/mod.rs` and `filesystem/gate.rs` to help maintainers keep them in sync. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
Update inline comments, documentation, and test-coverage matrix entries across the codebase to point to the new `tinytools-std` crate paths instead of the old `crates/openhuman-core/src/tools/impl/filesystem/` locations. The filesystem tool implementations were moved into the `tinytools-std` crate as part of a refactoring that extracted shared tool logic into a separate library, so all cross-references needed to be updated to keep the documentation accurate and prevent confusion when developers follow the links. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
The glob crate was removed from the dependency list in Cargo.toml and the corresponding entry in Cargo.lock, as it is no longer used by the crate. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
The tinyagents vendored dependency was updated to a new commit, and the Cargo.lock was adjusted to reflect the removal of the `glob` dependency from one crate while adding `fs2`, `glob`, `libc`, `regex`, and `walkdir` to another. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
The test for write tools being blocked in read-only mode was using the old CSV export API with a `path` field and inline data array. Updated it to match the current API which expects a `filename` field and a JSON-encoded string for the data parameter. Auto-committed-on: dragonfly Co-authored-by: Medulla <medulla@tinyhumans.ai>
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Navigate logical layers of code changes, visualize relationships, and explore their blast radius. 📝 WalkthroughWalkthroughFilesystem tool implementations and tests are removed from ChangesFilesystem tools migration
Vendored tinyagents revision
Priority: ➖ Normal Estimated code review effort: 4 (Complex) | ~45 minutes Change: Refactor Suggested reviewers: Merge Risk: 🔵 Low · up to The migration has no established merge-blocking defect. Correct the filesystem registration table so maintainers can accurately identify available tools. Security Architecture ReviewSecurity architecture risk: 🟡 Moderate · up to Security-sensitive filesystem operations move to a separate library. Access rules remain centrally defined, but consistent enforcement, shared action limits, and Git execution protections could not be fully verified. No new vulnerability was established; the remaining boundary uncertainty warrants moderate risk. Retained concerns Security review detailsSecurity Blast Radius
Trust Boundaries and Controls
Resilience and Maintainability Implications
Hardening Proposals
🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Docstring CoverageExplanation Docstring coverage is 57.89% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 38 functions across 20 files. (5 skipped: 5 unsupported.)
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Review comments at @crates/openhuman-core/src/tools/impl/README.md:
- Line 33: Update the filesystem registration-status entry in the README table:
state that ReadDiffTool, RunLinterTool, and RunTestsTool are registered as
Deferred, not “exported, not registered.”
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⛔ Files ignored due to path filters (2)
Cargo.lockis excluded by!**/*.lockcrates/openhuman-app/Cargo.lockis excluded by!**/*.lock
📒 Files selected for processing (55)
app/test/e2e/specs/harness-search-tool-flow.spec.tsapp/test/e2e/specs/tool-filesystem-flow.spec.tsapp/test/e2e/specs/tool-shell-git-flow.spec.tscrates/openhuman-core/Cargo.tomlcrates/openhuman-core/src/agent/harness/memory_protocol.rscrates/openhuman-core/src/agent/harness/tool_result_artifacts/mod.rscrates/openhuman-core/src/agent/session_host/artifact_wiring.rscrates/openhuman-core/src/agent/tinyagents/middleware/tool_output.rscrates/openhuman-core/src/agent/tinyagents/middleware_tool_output_artifact_tests.rscrates/openhuman-core/src/memory/guard/policy.rscrates/openhuman-core/src/security/policy/README.mdcrates/openhuman-core/src/security/policy/enforcement.rscrates/openhuman-core/src/tools/README.mdcrates/openhuman-core/src/tools/impl/README.mdcrates/openhuman-core/src/tools/impl/filesystem/apply_patch.rscrates/openhuman-core/src/tools/impl/filesystem/apply_patch_tests.rscrates/openhuman-core/src/tools/impl/filesystem/csv_export.rscrates/openhuman-core/src/tools/impl/filesystem/csv_export_tests.rscrates/openhuman-core/src/tools/impl/filesystem/edit_file.rscrates/openhuman-core/src/tools/impl/filesystem/edit_file_tests.rscrates/openhuman-core/src/tools/impl/filesystem/file_read.rscrates/openhuman-core/src/tools/impl/filesystem/file_read_tests.rscrates/openhuman-core/src/tools/impl/filesystem/file_write.rscrates/openhuman-core/src/tools/impl/filesystem/file_write_tests.rscrates/openhuman-core/src/tools/impl/filesystem/gate.rscrates/openhuman-core/src/tools/impl/filesystem/gate_tests.rscrates/openhuman-core/src/tools/impl/filesystem/git_operations.rscrates/openhuman-core/src/tools/impl/filesystem/git_operations_config.rscrates/openhuman-core/src/tools/impl/filesystem/git_operations_config_tests.rscrates/openhuman-core/src/tools/impl/filesystem/git_operations_render.rscrates/openhuman-core/src/tools/impl/filesystem/git_operations_tests.rscrates/openhuman-core/src/tools/impl/filesystem/glob_search.rscrates/openhuman-core/src/tools/impl/filesystem/glob_search_tests.rscrates/openhuman-core/src/tools/impl/filesystem/grep.rscrates/openhuman-core/src/tools/impl/filesystem/grep_tests.rscrates/openhuman-core/src/tools/impl/filesystem/list_files.rscrates/openhuman-core/src/tools/impl/filesystem/list_files_tests.rscrates/openhuman-core/src/tools/impl/filesystem/mod.rscrates/openhuman-core/src/tools/impl/filesystem/mod_tests.rscrates/openhuman-core/src/tools/impl/filesystem/read_diff.rscrates/openhuman-core/src/tools/impl/filesystem/read_diff_tests.rscrates/openhuman-core/src/tools/impl/filesystem/run_linter.rscrates/openhuman-core/src/tools/impl/filesystem/run_linter_tests.rscrates/openhuman-core/src/tools/impl/filesystem/run_tests.rscrates/openhuman-core/src/tools/impl/filesystem/update_memory_md.rscrates/openhuman-core/src/tools/impl/filesystem/update_memory_md_tests.rscrates/openhuman-core/src/tools/impl/filesystem/write_sink.rscrates/openhuman-core/src/tools/impl/mod.rscrates/openhuman-core/src/tools/impl/system/mod.rscrates/openhuman-core/src/tools/impl/system/shell.rscrates/openhuman-core/src/tools/ops.rscrates/openhuman-core/src/tools/ops_tests_domain_family_tests.rsdocs/TEST-COVERAGE-MATRIX.mdtests/agent_harness_e2e.rsvendor/tinyagents
💤 Files with no reviewable changes (30)
- crates/openhuman-core/src/tools/impl/filesystem/run_linter_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/list_files_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/git_operations_config_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/edit_file_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/csv_export_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/grep_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/apply_patch_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/read_diff_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/update_memory_md_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/file_read_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/read_diff.rs
- crates/openhuman-core/src/tools/impl/filesystem/csv_export.rs
- crates/openhuman-core/src/tools/impl/filesystem/git_operations.rs
- crates/openhuman-core/src/tools/impl/filesystem/file_write_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/glob_search_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/git_operations_render.rs
- crates/openhuman-core/src/tools/impl/filesystem/grep.rs
- crates/openhuman-core/src/tools/impl/filesystem/write_sink.rs
- crates/openhuman-core/src/tools/impl/filesystem/list_files.rs
- crates/openhuman-core/src/tools/impl/filesystem/git_operations_tests.rs
- crates/openhuman-core/Cargo.toml
- crates/openhuman-core/src/tools/impl/filesystem/file_write.rs
- crates/openhuman-core/src/tools/impl/filesystem/apply_patch.rs
- crates/openhuman-core/src/tools/impl/filesystem/edit_file.rs
- crates/openhuman-core/src/tools/impl/filesystem/file_read.rs
- crates/openhuman-core/src/tools/impl/filesystem/run_tests.rs
- crates/openhuman-core/src/tools/impl/filesystem/glob_search.rs
- crates/openhuman-core/src/tools/impl/filesystem/git_operations_config.rs
- crates/openhuman-core/src/tools/impl/filesystem/update_memory_md.rs
- crates/openhuman-core/src/tools/impl/filesystem/run_linter.rs
Included review availability: This review used your included allowance. Your plan provides up to 10 included reviews per hour; 8 remain after this review.
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| | `system/` | `ShellTool`, `NodeExecTool`, `NpmExecTool`, `PythonExecTool`, `InstallToolTool`, `DetectToolsTool` (from `tinytools_std`), `CurrentTimeTool` and `ResolveTimeTool` (imported directly from `tinyagents_harness::tools` at their call sites; no local copy), `ScheduleTool`, `ProxyConfigTool`, `PushoverTool`, `LspTool`, `ToolStatsTool`, `UpdateCheckTool`, `UpdateApplyTool`, `InsertSqlRecordTool`, `WorkspaceStateTool`, `RetrieveToolOutputTool`; shell failure rendering lives in `tinytools_std::command_output` | `node_exec`/`npm_exec` and `shell`'s PATH injection need the `runtime-node` Cargo feature plus `node.enabled`; `python_exec` needs `runtime_python.enabled`; `LspTool` needs `OPENHUMAN_LSP_ENABLED` (`lsp_capability_enabled`); `ToolStatsTool` needs `learning.enabled` and `learning.tool_tracking_enabled`; `InsertSqlRecordTool` is exported, not registered; the rest are always registered | | ||
| | `filesystem/` | `FileReadTool`, `FileWriteTool`, `EditFileTool`, `ApplyPatchTool`, `GrepTool`, `GlobTool`, `ListFilesTool`, `ReadDiffTool`, `CsvExportTool`, `GitOperationsTool`, `RunLinterTool`, `RunTestsTool`, `UpdateMemoryMdTool` | always registered, except `ReadDiffTool`, `RunLinterTool`, and `RunTestsTool`, which are exported, not registered | | ||
| | `filesystem/` | Host adapter only: `SecurityPolicy` implements `tinytools_std::filesystem::FsGate`. The tools (`FileReadTool`, `FileWriteTool`, `EditFileTool`, `ApplyPatchTool`, `GrepTool`, `GlobTool`, `ListFilesTool`, `ReadDiffTool`, `CsvExportTool`, `GitOperationsTool`, `RunLinterTool`, `RunTestsTool`, `UpdateMemoryMdTool`) live in `tinytools_std::filesystem` and are imported directly by `tools/ops.rs` | always registered, except `ReadDiffTool`, `RunLinterTool`, and `RunTestsTool`, which are exported, not registered | |
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📐 Maintainability & Code Quality | 🟡 Minor | ⚡ Quick win
Correct the registration status in the table.
The table says that ReadDiffTool, RunLinterTool, and RunTestsTool are "exported, not registered". This statement is wrong. tools/ops.rs registers all three tools at lines 465-473. The file header defines "exported, not registered" as a struct that no production assembly site constructs. Update the table to say that these three tools are registered as Deferred.
Proposed fix
-| ... | always registered, except `ReadDiffTool`, `RunLinterTool`, and `RunTestsTool`, which are exported, not registered |
+| ... | always registered; `ReadDiffTool`, `RunLinterTool`, and `RunTestsTool` are registered as `Deferred` |📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
Suggested change
| | `filesystem/` | Host adapter only: `SecurityPolicy` implements `tinytools_std::filesystem::FsGate`. The tools (`FileReadTool`, `FileWriteTool`, `EditFileTool`, `ApplyPatchTool`, `GrepTool`, `GlobTool`, `ListFilesTool`, `ReadDiffTool`, `CsvExportTool`, `GitOperationsTool`, `RunLinterTool`, `RunTestsTool`, `UpdateMemoryMdTool`) live in `tinytools_std::filesystem` and are imported directly by `tools/ops.rs` | always registered, except `ReadDiffTool`, `RunLinterTool`, and `RunTestsTool`, which are exported, not registered | | |
| | `filesystem/` | Host adapter only: `SecurityPolicy` implements `tinytools_std::filesystem::FsGate`. The tools (`FileReadTool`, `FileWriteTool`, `EditFileTool`, `ApplyPatchTool`, `GrepTool`, `GlobTool`, `ListFilesTool`, `ReadDiffTool`, `CsvExportTool`, `GitOperationsTool`, `RunLinterTool`, `RunTestsTool`, `UpdateMemoryMdTool`) live in `tinytools_std::filesystem` and are imported directly by `tools/ops.rs` | always registered; `ReadDiffTool`, `RunLinterTool`, and `RunTestsTool` are registered as `Deferred` | |
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Review comment at @crates/openhuman-core/src/tools/impl/README.md at line 33:
Update the filesystem registration-status entry in the README table: state that
ReadDiffTool, RunLinterTool, and RunTestsTool are registered as Deferred, not
“exported, not registered.”
After applying the fix, consider running `coderabbit review --agent` for local
review. Visit https://docs.coderabbit.ai/cli?utm_source=ghpr
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Summary
Wave 3 moves the 13 filesystem tools into
tinytools-std, behind a newFsGatetrait. OpenHuman keeps only the policy adapter. The net change is −7.3k lines (517 added, 7,800 deleted).The
FsGateseamFsGateis object-safe (Send + Sync + Debug) and asks only the questions the tools need:can_act,is_read_only,is_rate_limitedandrecord_actionwrite_needs_approvalandaction_diris_path_string_allowed,validate_pathandvalidate_parent_pathscoped_to_workspace(root)It has no decision types of its own. The adapter
tools/impl/filesystem/gate.rsimplements it forSecurityPolicy, so every policy stays in OpenHuman: autonomy, the always-forbidden floor,workspace_only, trusted roots, approvals and the action budget.tools/ops.rsstill registers the tools.security_scoped_to_rootis the oldsecurity_for_tool_contextgrant, moved unchanged.Moved to
tinytools_std::filesystem(tinytools#38, gitlink bump in tinyagents#245)file_read,file_write,edit_file,apply_patch,grep,glob_search,list_files,csv_export,git_operations,read_diff,run_linter,run_testsandupdate_memory_md.filesystemfile is at 91.7%.gate_tests.rs: symlink escape, traversal, read-only, rate limits, approval flags and the workspace grant.60e9194, the tip of the pin-based branch. fixes: conversation fixes #38's head additionally merges tinytoolsmain(0.5.0, wherefile_state::record_readtakes anInstant) with that one adaptation. The unused coreglobdependency is removed.Verification
cargo check --tests -p openhuman -p openhuman-cli --features "$(bash scripts/ci/product-features.sh)"is clean, and so are the app manifest and embed/tinyhumans.raw_coverage_all: 157 passed, 1 failed (known MCP).agent_harness_e2e: 22 passed, 3 failed, all known and reproduced onmain.tinytools-stdhas 369 tests on the merged branch and 343 at the pin. fmt,clippy -D warnings,cargo doc -D warningsand the coverage gate all pass.check-feature-forwarding,check-gated-test-allowlistandcheck-submodule-monotonicpass. This PR adds no new boundary or layout violations.Failures that are already on
mainThese reproduce on
main, and every one of them was also checked at an earlier baseline:agent::goals::tools::tests::set_persists_to_the_workspace_store_and_answers_goal_and_text, fixed in test(goals): read structured goal tool results via output() #6803.raw_coverage_all: the MCP testtool_registry_entries_include_connected_mcp_client_tools.agent_harness_e2e:orchestrator_advertises_direct_mcp_tools,orchestrator_cannot_install_a_skill_through_the_raw_registry_toolandorchestrator_hands_skill_installs_to_skill_setup_directly. These fail identically ate80051674e, the test: drop 45 quarantined raw-coverage files, dedupe vendor-covered tests, repoint vendor pins #6781 merge, which is before any of the vendor-extraction PRs.rust:layout:runtime_session.rsis 1994 lines against a limit of 1990.openhuman_backend_model{,_tests}.rsare 759 and 761 against 750.check-agent-runtime-boundary: the existing violations inopenhuman_backend_model.rs,json_schema/ops.rsandtools/impl/meta/mod.rs.check-module-pins: tinychannels.Summary by CodeRabbit