Commit Graph

198 Commits

  • chore: cleanup Config instantiation codepaths (#8226)
    This PR does various types of cleanup before I can proceed with more
    ambitious changes to config loading.
    
    First, I noticed duplicated code across these two methods:
    
    
    https://github.com/openai/codex/blob/774bd9e432fa2e0f4e059e97648cf92216912e19/codex-rs/core/src/config/mod.rs#L314-L324
    
    
    https://github.com/openai/codex/blob/774bd9e432fa2e0f4e059e97648cf92216912e19/codex-rs/core/src/config/mod.rs#L334-L344
    
    This has now been consolidated in
    `load_config_as_toml_with_cli_overrides()`.
    
    Further, I noticed that `Config::load_with_cli_overrides()` took two
    similar arguments:
    
    
    https://github.com/openai/codex/blob/774bd9e432fa2e0f4e059e97648cf92216912e19/codex-rs/core/src/config/mod.rs#L308-L311
    
    The difference between `cli_overrides` and `overrides` was not
    immediately obvious to me. At first glance, it appears that one should
    be able to be expressed in terms of the other, but it turns out that
    some fields of `ConfigOverrides` (such as `cwd` and
    `codex_linux_sandbox_exe`) are, by design, not configurable via a
    `.toml` file or a command-line `--config` flag.
    
    That said, I discovered that many callers of
    `Config::load_with_cli_overrides()` were passing
    `ConfigOverrides::default()` for `overrides`, so I created two separate
    methods:
    
    - `Config::load_with_cli_overrides(cli_overrides: Vec<(String,
    TomlValue)>)`
    - `Config::load_with_cli_overrides_and_harness_overrides(cli_overrides:
    Vec<(String, TomlValue)>, harness_overrides: ConfigOverrides)`
    
    The latter has a long name, as it is _not_ what should be used in the
    common case, so the extra typing is designed to draw attention to this
    fact. I tried to update the existing callsites to use the shorter name,
    where possible.
    
    Further, in the cases where `ConfigOverrides` is used, usually only a
    limited subset of fields are actually set, so I updated the declarations
    to leverage `..Default::default()` where possible.
  • Add public skills + improve repo skill discovery and error UX (#8098)
    1. Adds SkillScope::Public end-to-end (core + protocol) and loads skills
    from the public cache directory
    2. Improves repo skill discovery by searching upward for the nearest
    .codex/skills within a git repo
    3. Deduplicates skills by name with deterministic ordering to avoid
    duplicates across sources
    4. Fixes garbled “Skill errors” overlay rendering by preventing pending
    history lines from being injected during the modal
    5. Updates the project docs “Skills” intro wording to avoid hardcoded
    paths
  • Reimplement skills loading using SkillsManager + skills/list op. (#7914)
    refactor the way we load and manage skills:
    1. Move skill discovery/caching into SkillsManager and reuse it across
    sessions.
    2. Add the skills/list API (Op::ListSkills/SkillsListResponse) to fetch
    skills for one or more cwds. Also update app-server for VSCE/App;
    3. Trigger skills/list during session startup so UIs preload skills and
    handle errors immediately.
  • Inject SKILL.md when it's explicitly mentioned. (#7763)
    1. Skills load once in core at session start; the cached outcome is
    reused across core and surfaced to TUI via SessionConfigured.
    2. TUI detects explicit skill selections, and core injects the matching
    SKILL.md content into the turn when a selected skill is present.
  • Removed experimental "command risk assessment" feature (#7799)
    This experimental feature received lukewarm reception during internal
    testing. Removing from the code base.
  • Refactor execpolicy fallback evaluation (#7544)
    ## Refactor of the `execpolicy` crate
    
    To illustrate why we need this refactor, consider an agent attempting to
    run `apple | rm -rf ./`. Suppose `apple` is allowed by `execpolicy`.
    Before this PR, `execpolicy` would consider `apple` and `pear` and only
    render one rule match: `Allow`. We would skip any heuristics checks on
    `rm -rf ./` and immediately approve `apple | rm -rf ./` to run.
    
    To fix this, we now thread a `fallback` evaluation function into
    `execpolicy` that runs when no `execpolicy` rules match a given command.
    In our example, we would run `fallback` on `rm -rf ./` and prevent
    `apple | rm -rf ./` from being run without approval.
  • whitelist command prefix integration in core and tui (#7033)
    this PR enables TUI to approve commands and add their prefixes to an
    allowlist:
    <img width="708" height="605" alt="Screenshot 2025-11-21 at 4 18 07 PM"
    src="https://github.com/user-attachments/assets/56a19893-4553-4770-a881-becf79eeda32"
    />
    
    note: we only show the option to whitelist the command when 
    1) command is not multi-part (e.g `git add -A && git commit -m 'hello
    world'`)
    2) command is not already matched by an existing rule
  • Migrate model preset (#7542)
    - Introduce `openai_models` in `/core`
    - Move `PRESETS` under it
    - Move `ModelPreset`, `ModelUpgrade`, `ReasoningEffortPreset`,
    `ReasoningEffortPreset`, and `ReasoningEffortPreset` to `protocol`
    - Introduce `Op::ListModels` and `EventMsg::AvailableModels`
    
    Next steps:
    - migrate `app-server` and `tui` to use the introduced Operation
  • chore: add cargo-deny configuration (#7119)
    - add GitHub workflow running cargo-deny on push/PR
    - document cargo-deny allowlist with workspace-dep notes and advisory
    ignores
    - align workspace crates to inherit version/edition/license for
    consistent checks
  • support MCP elicitations (#6947)
    No support for request schema yet, but we'll at least show the message
    and allow accept/decline.
    
    <img width="823" height="551" alt="Screenshot 2025-11-21 at 2 44 05 PM"
    src="https://github.com/user-attachments/assets/6fbb892d-ca12-4765-921e-9ac4b217534d"
    />
  • [app-server] feat: v2 apply_patch approval flow (#6760)
    This PR adds the API V2 version of the apply_patch approval flow, which
    centers around `ThreadItem::FileChange`.
    
    This PR wires the new RPC (`item/fileChange/requestApproval`, V2 only)
    and related events (`item/started`, `item/completed` for
    `ThreadItem::FileChange`, which are emitted in both V1 and V2) through
    the app-server
    protocol. The new approval RPC is only sent when the user initiates a
    turn with the new `turn/start` API so we don't break backwards
    compatibility with VSCE.
    
    Similar to https://github.com/openai/codex/pull/6758, the approach I
    took was to make as few changes to the Codex core as possible,
    leveraging existing `EventMsg` core events, and translating those in
    app-server. I did have to add a few additional fields to
    `EventMsg::PatchApplyBegin` and `EventMsg::PatchApplyEnd`, but those
    were fairly lightweight.
    
    However, the `EventMsg`s emitted by core are the following:
    ```
    1) Auto-approved (no request for approval)

    - EventMsg::PatchApplyBegin
    - EventMsg::PatchApplyEnd
    
    2) Approved by user
    - EventMsg::ApplyPatchApprovalRequest
    - EventMsg::PatchApplyBegin
    - EventMsg::PatchApplyEnd
    
    3) Declined by user
    - EventMsg::ApplyPatchApprovalRequest
    - EventMsg::PatchApplyBegin
    - EventMsg::PatchApplyEnd
    ```
    
    For a request triggering an approval, this would result in:
    ```
    item/fileChange/requestApproval
    item/started
    item/completed
    ```
    
    which is different from the `ThreadItem::CommandExecution` flow
    introduced in https://github.com/openai/codex/pull/6758, which does the
    below and is preferable:
    ```
    item/started
    item/commandExecution/requestApproval
    item/completed
    ```
    
    To fix this, we leverage `TurnSummaryStore` on codex_message_processor
    to store a little bit of state, allowing us to fire `item/started` and
    `item/fileChange/requestApproval` whenever we receive the underlying
    `EventMsg::ApplyPatchApprovalRequest`, and no-oping when we receive the
    `EventMsg::PatchApplyBegin` later.
    
    This is much less invasive than modifying the order of EventMsg within
    core (I tried).
    
    The resulting payloads:
    ```
    {
      "method": "item/started",
      "params": {
        "item": {
          "changes": [
            {
              "diff": "Hello from Codex!\n",
              "kind": "add",
              "path": "/Users/owen/repos/codex/codex-rs/APPROVAL_DEMO.txt"
            }
          ],
          "id": "call_Nxnwj7B3YXigfV6Mwh03d686",
          "status": "inProgress",
          "type": "fileChange"
        }
      }
    }
    ```
    
    ```
    {
      "id": 0,
      "method": "item/fileChange/requestApproval",
      "params": {
        "grantRoot": null,
        "itemId": "call_Nxnwj7B3YXigfV6Mwh03d686",
        "reason": null,
        "threadId": "019a9e11-8295-7883-a283-779e06502c6f",
        "turnId": "1"
      }
    }
    ```
    
    ```
    {
      "id": 0,
      "result": {
        "decision": "accept"
      }
    }
    ```
    
    ```
    {
      "method": "item/completed",
      "params": {
        "item": {
          "changes": [
            {
              "diff": "Hello from Codex!\n",
              "kind": "add",
              "path": "/Users/owen/repos/codex/codex-rs/APPROVAL_DEMO.txt"
            }
          ],
          "id": "call_Nxnwj7B3YXigfV6Mwh03d686",
          "status": "completed",
          "type": "fileChange"
        }
      }
    }
    ```
  • fix: add more fields to ThreadStartResponse and ThreadResumeResponse (#6847)
    This adds the following fields to `ThreadStartResponse` and
    `ThreadResumeResponse`:
    
    ```rust
        pub model: String,
        pub model_provider: String,
        pub cwd: PathBuf,
        pub approval_policy: AskForApproval,
        pub sandbox: SandboxPolicy,
        pub reasoning_effort: Option<ReasoningEffort>,
    ```
    
    This is important because these fields are optional in
    `ThreadStartParams` and `ThreadResumeParams`, so the caller needs to be
    able to determine what values were ultimately used to start/resume the
    conversation. (Though note that any of these could be changed later
    between turns in the conversation.)
    
    Though to get this information reliably, it must be read from the
    internal `SessionConfiguredEvent` that is created in response to the
    start of a conversation. Because `SessionConfiguredEvent` (as defined in
    `codex-rs/protocol/src/protocol.rs`) did not have all of these fields, a
    number of them had to be added as part of this PR.
    
    Because `SessionConfiguredEvent` is referenced in many tests, test
    instances of `SessionConfiguredEvent` had to be updated, as well, which
    is why this PR touches so many files.
  • [app-server] feat: add v2 command execution approval flow (#6758)
    This PR adds the API V2 version of the command‑execution approval flow
    for the shell tool.
    
    This PR wires the new RPC (`item/commandExecution/requestApproval`, V2
    only) and related events (`item/started`, `item/completed`, and
    `item/commandExecution/delta`, which are emitted in both V1 and V2)
    through the app-server
    protocol. The new approval RPC is only sent when the user initiates a
    turn with the new `turn/start` API so we don't break backwards
    compatibility with VSCE.
    
    The approach I took was to make as few changes to the Codex core as
    possible, leveraging existing `EventMsg` core events, and translating
    those in app-server. I did have to add additional fields to
    `EventMsg::ExecCommandEndEvent` to capture the command's input so that
    app-server can statelessly transform these events to a
    `ThreadItem::CommandExecution` item for the `item/completed` event.
    
    Once we stabilize the API and it's complete enough for our partners, we
    can work on migrating the core to be aware of command execution items as
    a first-class concept.
    
    **Note**: We'll need followup work to make sure these APIs work for the
    unified exec tool, but will wait til that's stable and landed before
    doing a pass on app-server.
    
    Example payloads below:
    ```
    {
      "method": "item/started",
      "params": {
        "item": {
          "aggregatedOutput": null,
          "command": "/bin/zsh -lc 'touch /tmp/should-trigger-approval'",
          "cwd": "/Users/owen/repos/codex/codex-rs",
          "durationMs": null,
          "exitCode": null,
          "id": "call_lNWWsbXl1e47qNaYjFRs0dyU",
          "parsedCmd": [
            {
              "cmd": "touch /tmp/should-trigger-approval",
              "type": "unknown"
            }
          ],
          "status": "inProgress",
          "type": "commandExecution"
        }
      }
    }
    ```
    
    ```
    {
      "id": 0,
      "method": "item/commandExecution/requestApproval",
      "params": {
        "itemId": "call_lNWWsbXl1e47qNaYjFRs0dyU",
        "parsedCmd": [
          {
            "cmd": "touch /tmp/should-trigger-approval",
            "type": "unknown"
          }
        ],
        "reason": "Need to create file in /tmp which is outside workspace sandbox",
        "risk": null,
        "threadId": "019a93e8-0a52-7fe3-9808-b6bc40c0989a",
        "turnId": "1"
      }
    }
    ```
    
    ```
    {
      "id": 0,
      "result": {
        "acceptSettings": {
          "forSession": false
        },
        "decision": "accept"
      }
    }
    ```
    
    ```
    {
      "params": {
        "item": {
          "aggregatedOutput": null,
          "command": "/bin/zsh -lc 'touch /tmp/should-trigger-approval'",
          "cwd": "/Users/owen/repos/codex/codex-rs",
          "durationMs": 224,
          "exitCode": 0,
          "id": "call_lNWWsbXl1e47qNaYjFRs0dyU",
          "parsedCmd": [
            {
              "cmd": "touch /tmp/should-trigger-approval",
              "type": "unknown"
            }
          ],
          "status": "completed",
          "type": "commandExecution"
        }
      }
    }
    ```
  • core/tui: non-blocking MCP startup (#6334)
    This makes MCP startup not block TUI startup. Messages sent while MCPs
    are booting will be queued.
    
    
    https://github.com/user-attachments/assets/96e1d234-5d8f-4932-a935-a675d35c05e0
    
    
    Fixes #6317
    
    ---------
    
    Co-authored-by: pakrym-oai <pakrym@openai.com>
  • Add warning on compact (#6052)
    This PR introduces the ability for `core` to send `warnings` as it can
    send `errors. It also sends a warning on compaction.
    
    <img width="811" height="187" alt="image"
    src="https://github.com/user-attachments/assets/0947a42d-b720-420d-b7fd-115f8a65a46a"
    />
  • [Hygiene] Remove include_view_image_tool config (#5976)
    There's still some debate about whether we want to expose
    `tools.view_image` or `feature.view_image` so those are left unchanged
    for now, but this old `include_view_image_tool` config is good-to-go.
    Also updated the doc to reflect that `view_image` tool is now by default
    true.
  • [codex] add developer instructions (#5897)
    we are using developer instructions for code reviews, we need to pass
    them in cli as well.
  • feat: compaction prompt configurable (#5959)
    ```
     codex -c compact_prompt="Summarize in bullet points"
     ```
  • Add item streaming events (#5546)
    Adds AgentMessageContentDelta, ReasoningContentDelta,
    ReasoningRawContentDelta item streaming events while maintaining
    compatibility for old events.
    
    ---------
    
    Co-authored-by: Owen Lin <owen@openai.com>
  • feat: deprecation warning (#5825)
    <img width="955" height="311" alt="Screenshot 2025-10-28 at 14 26 25"
    src="https://github.com/user-attachments/assets/99729b3d-3bc9-4503-aab3-8dc919220ab4"
    />
  • [Auth] Choose which auth storage to use based on config (#5792)
    This PR is a follow-up to #5591. It allows users to choose which auth
    storage mode they want by using the new
    `cli_auth_credentials_store_mode` config.
  • Added model summary and risk assessment for commands that violate sandbox policy (#5536)
    This PR adds support for a model-based summary and risk assessment for
    commands that violate the sandbox policy and require user approval. This
    aids the user in evaluating whether the command should be approved.
    
    The feature works by taking a failed command and passing it back to the
    model and asking it to summarize the command, give it a risk level (low,
    medium, high) and a risk category (e.g. "data deletion" or "data
    exfiltration"). It uses a new conversation thread so the context in the
    existing thread doesn't influence the answer. If the call to the model
    fails or takes longer than 5 seconds, it falls back to the current
    behavior.
    
    For now, this is an experimental feature and is gated by a config key
    `experimental_sandbox_command_assessment`.
    
    Here is a screen shot of the approval prompt showing the risk assessment
    and summary.
    
    <img width="723" height="282" alt="image"
    src="https://github.com/user-attachments/assets/4597dd7c-d5a0-4e9f-9d13-414bd082fd6b"
    />
  • Enable plan tool by default (#5384)
    ## Summary
    - make the plan tool available by default by removing the feature flag
    and always registering the handler
    - drop plan-tool CLI and API toggles across the exec, TUI, MCP server,
    and app server code paths
    - update tests and configs to reflect the always-on plan tool and guard
    workspace restriction tests against env leakage
    
    ## Testing
    Manually tested the extension. 
    ------
    https://chatgpt.com/codex/tasks/task_i_68f67a3ff2d083209562a773f814c1f9
  • Add ItemStarted/ItemCompleted events for UserInputItem (#5306)
    Adds a new ItemStarted event and delivers UserMessage as the first item
    type (more to come).
    
    
    Renames `InputItem` to `UserInput` considering we're using the `Item`
    suffix for actual items.
  • chore: rework tools execution workflow (#5278)
    Re-work the tool execution flow. Read `orchestrator.rs` to understand
    the structure
  • feat: add --add-dir flag for extra writable roots (#5335)
    Add a `--add-dir` CLI flag so sessions can use extra writable roots in
    addition to the ones specified in the config file. These are ephemerally
    added during the session only.
    
    Fixes #3303
    Fixes #2797
  • feat: add Vec<ParsedCommand> to ExecApprovalRequestEvent (#5222)
    This adds `parsed_cmd: Vec<ParsedCommand>` to `ExecApprovalRequestEvent`
    in the core protocol (`protocol/src/protocol.rs`), which is also what
    this field is named on `ExecCommandBeginEvent`. Honestly, I don't love
    the name (it sounds like a single command, but it is actually a list of
    them), but I don't want to get distracted by a naming discussion right
    now.
    
    This also adds `parsed_cmd` to `ExecCommandApprovalParams` in
    `codex-rs/app-server-protocol/src/protocol.rs`, so it will be available
    via `codex app-server`, as well.
    
    For consistency, I also updated `ExecApprovalElicitRequestParams` in
    `codex-rs/mcp-server/src/exec_approval.rs` to include this field under
    the name `codex_parsed_cmd`, as that struct already has a number of
    special `codex_*` fields. Note this is the code for when Codex is used
    as an MCP _server_ and therefore has to conform to the official spec for
    an MCP elicitation type.
  • revert /name for now (#4978)
    There was a regression where we'd read entire rollout contents if there
    was no /name present.
  • feat: Set chat name (#4974)
    Set chat name with `/name` so they appear in the codex resume page:
    
    
    https://github.com/user-attachments/assets/c0252bba-3a53-44c7-a740-f4690a3ad405
  • add(core): managed config (#3868)
    ## Summary
    
    - Factor `load_config_as_toml` into `core::config_loader` so config
    loading is reusable across callers.
    - Layer `~/.codex/config.toml`, optional `~/.codex/managed_config.toml`,
    and macOS managed preferences (base64) with recursive table merging and
    scoped threads per source.
    
    ## Config Flow
    
    ```
    Managed prefs (macOS profile: com.openai.codex/config_toml_base64)
                                   ▲
                                   │
    ~/.codex/managed_config.toml   │  (optional file-based override)
                                   ▲
                                   │
                    ~/.codex/config.toml (user-defined settings)
    ```
    
    - The loader searches under the resolved `CODEX_HOME` directory
    (defaults to `~/.codex`).
    - Managed configs let administrators ship fleet-wide overrides via
    device profiles which is useful for enforcing certain settings like
    sandbox or approval defaults.
    - For nested hash tables: overlays merge recursively. Child tables are
    merged key-by-key, while scalar or array values replace the prior layer
    entirely. This lets admins add or tweak individual fields without
    clobbering unrelated user settings.
  • Separate interactive and non-interactive sessions (#4612)
    Do not show exec session in VSCode/TUI selector.
  • Support CODEX_API_KEY for codex exec (#4615)
    Allows to set API key per invocation of `codex exec`
  • fix: remove mcp-types from app server protocol (#4537)
    We continue the separation between `codex app-server` and `codex
    mcp-server`.
    
    In particular, we introduce a new crate, `codex-app-server-protocol`,
    and migrate `codex-rs/protocol/src/mcp_protocol.rs` into it, renaming it
    `codex-rs/app-server-protocol/src/protocol.rs`.
    
    Because `ConversationId` was defined in `mcp_protocol.rs`, we move it
    into its own file, `codex-rs/protocol/src/conversation_id.rs`, and
    because it is referenced in a ton of places, we have to touch a lot of
    files as part of this PR.
    
    We also decide to get away from proper JSON-RPC 2.0 semantics, so we
    also introduce `codex-rs/app-server-protocol/src/jsonrpc_lite.rs`, which
    is basically the same `JSONRPCMessage` type defined in `mcp-types`
    except with all of the `"jsonrpc": "2.0"` removed.
    
    Getting rid of `"jsonrpc": "2.0"` makes our serialization logic
    considerably simpler, as we can lean heavier on serde to serialize
    directly into the wire format that we use now.
  • fix: separate codex mcp into codex mcp-server and codex app-server (#4471)
    This is a very large PR with some non-backwards-compatible changes.
    
    Historically, `codex mcp` (or `codex mcp serve`) started a JSON-RPC-ish
    server that had two overlapping responsibilities:
    
    - Running an MCP server, providing some basic tool calls.
    - Running the app server used to power experiences such as the VS Code
    extension.
    
    This PR aims to separate these into distinct concepts:
    
    - `codex mcp-server` for the MCP server
    - `codex app-server` for the "application server"
    
    Note `codex mcp` still exists because it already has its own subcommands
    for MCP management (`list`, `add`, etc.)
    
    The MCP logic continues to live in `codex-rs/mcp-server` whereas the
    refactored app server logic is in the new `codex-rs/app-server` folder.
    Note that most of the existing integration tests in
    `codex-rs/mcp-server/tests/suite` were actually for the app server, so
    all the tests have been moved with the exception of
    `codex-rs/mcp-server/tests/suite/mod.rs`.
    
    Because this is already a large diff, I tried not to change more than I
    had to, so `codex-rs/app-server/tests/common/mcp_process.rs` still uses
    the name `McpProcess` for now, but I will do some mechanical renamings
    to things like `AppServer` in subsequent PRs.
    
    While `mcp-server` and `app-server` share some overlapping functionality
    (like reading streams of JSONL and dispatching based on message types)
    and some differences (completely different message types), I ended up
    doing a bit of copypasta between the two crates, as both have somewhat
    similar `message_processor.rs` and `outgoing_message.rs` files for now,
    though I expect them to diverge more in the near future.
    
    One material change is that of the initialize handshake for `codex
    app-server`, as we no longer use the MCP types for that handshake.
    Instead, we update `codex-rs/protocol/src/mcp_protocol.rs` to add an
    `Initialize` variant to `ClientRequest`, which takes the `ClientInfo`
    object we need to update the `USER_AGENT_SUFFIX` in
    `codex-rs/app-server/src/message_processor.rs`.
    
    One other material change is in
    `codex-rs/app-server/src/codex_message_processor.rs` where I eliminated
    a use of the `send_event_as_notification()` method I am generally trying
    to deprecate (because it blindly maps an `EventMsg` into a
    `JSONNotification`) in favor of `send_server_notification()`, which
    takes a `ServerNotification`, as that is intended to be a custom enum of
    all notification types supported by the app server. So to make this
    update, I had to introduce a new variant of `ServerNotification`,
    `SessionConfigured`, which is a non-backwards compatible change with the
    old `codex mcp`, and clients will have to be updated after the next
    release that contains this PR. Note that
    `codex-rs/app-server/tests/suite/list_resume.rs` also had to be update
    to reflect this change.
    
    I introduced `codex-rs/utils/json-to-toml/src/lib.rs` as a small utility
    crate to avoid some of the copying between `mcp-server` and
    `app-server`.
  • [mcp-server] Expose fuzzy file search in MCP (#2677)
    ## Summary
    Expose a simple fuzzy file search implementation for mcp clients to work
    with
    
    ## Testing
    - [x] Tested locally
  • make tests pass cleanly in sandbox (#4067)
    This changes the reqwest client used in tests to be sandbox-friendly,
    and skips a bunch of other tests that don't work inside the
    sandbox/without network.
  • Add exec output-schema parameter (#4079)
    Adds structured output to `exec` via the `--structured-output`
    parameter.
  • feat: update default (#4076)
    Changes:
    - Default model and docs now use gpt-5-codex. 
    - Disables the GPT-5 Codex NUX by default.
    - Keeps presets available for API key users.
  • chore: clippy on redundant closure (#4058)
    Add redundant closure clippy rules and let Codex fix it by minimising
    FQP
  • chore: unify cargo versions (#4044)
    Unify cargo versions at root