@rethunk/mcp-multi-root-git 2.4.0 → 2.6.0

package/docs/mcp-tools.md

@@ -15,9 +15,9 @@ MCP clients expose tools as `{serverName}_{toolName}`. With the server registere
 | `git_inventory` | `rethunk-git_git_inventory` | Status + ahead/behind per path; default upstream each repo’s `@{u}`; pass **both** `remote` and `branch` for fixed tracking. `nestedRoots`, `preset`, `presetMerge`, `maxRoots`, `format`, plus workspace pick args (`absoluteGitRoots` cannot combine with `preset`/`nestedRoots`). **Read-only.** |
 | `git_parity` | `rethunk-git_git_parity` | Compare `git rev-parse HEAD` for path pairs. `pairs`, `preset`, `presetMerge`, `format`, plus workspace pick args (`absoluteGitRoots` for sibling clone batches). **Read-only.** |
 | `list_presets` | `rethunk-git_list_presets` | List preset names/counts from `.rethunk/git-mcp-presets.json`; invalid JSON/schema surface as errors. Workspace pick + `format` only (includes `absoluteGitRoots`). **Read-only.** |
-| `git_log` | `rethunk-git_git_log` | Path-filtered, time-windowed `git log` across one or more workspace roots. Returns commit history with author, date, subject, and shortstat. Args: `since`, `paths`, `grep`, `author`, `maxCommits`, `branch`, plus workspace pick args (`absoluteGitRoots` for sibling clones) + `format`. **Read-only.** |
+| `git_log` | `rethunk-git_git_log` | Path-filtered, time-windowed `git log` across one or more workspace roots. Returns commit history with author, date, subject, and shortstat. Args: `since`, `paths`, `grep`, `author`, `maxCommits`, `branch`, plus workspace pick args (`absoluteGitRoots` for sibling clones) + `format` (`markdown`/`json`/`oneline`). **Read-only.** |
 | `git_diff_summary` | `rethunk-git_git_diff_summary` | Structured, token-efficient diff viewer. Returns per-file diffs with additions/deletions counts, truncated to configurable line limits, with lock files/dist/vendor excluded by default. Args: `range`, `fileFilter`, `maxLinesPerFile`, `maxFiles`, `excludePatterns`, plus workspace pick args (optional single-entry `absoluteGitRoots`) + `format`. **Read-only.** |
-| `git_diff` | `rethunk-git_git_diff` | Raw diff text for a single repo. Supports unstaged, staged, or `base..head` ranges, optionally scoped to one path. Args: `base?`, `head?`, `path?`, `staged?`, plus single-repo workspace pick + `format`. **Read-only.** |
+| `git_diff` | `rethunk-git_git_diff` | Raw diff text for a single repo. Supports unstaged, staged, or `base..head` ranges, optionally scoped to one path. Args: `workspaceRoot`, `rootIndex`, `format`, `base?`, `head?`, `path?`, `staged?`. No `absoluteGitRoots` or `allWorkspaceRoots`. **Read-only.** |
 | `git_show` | `rethunk-git_git_show` | Inspect one commit or ref. Returns commit message plus diff, or file content at `path` for that ref. Args: `ref`, `path?`, plus single-repo workspace pick + `format`. **Read-only.** |
 | `git_worktree_list` | `rethunk-git_git_worktree_list` | List all worktrees (`git worktree list --porcelain`). Workspace pick + `format`. **Read-only.** |
 | `git_stash_list` | `rethunk-git_git_stash_list` | List `git stash` entries for one repo. Args: single-repo workspace pick + `format`. **Read-only.** |
@@ -29,14 +29,237 @@ MCP clients expose tools as `{serverName}_{toolName}`. With the server registere
 | `git_reset_soft` | `rethunk-git_git_reset_soft` | Soft-reset the current branch to a ref (`HEAD~N`, SHA, branch). Rewound changes land in the staging index; requires a clean working tree. Args: `ref`, plus workspace pick + `format`. **Mutating — not idempotent.** |
 | `batch_commit` | `rethunk-git_batch_commit` | Create multiple sequential git commits in a single call. Each entry stages the listed files or line-ranged file hunks, then commits with the given message. Stops on first failure. Optional `push: "after"` pushes once every commit lands; optional `dryRun: true` previews staged content without writing commits. Args: `commits` (array of `{message, files}`), `push?`, `dryRun?`, plus workspace pick args + `format`. **Mutating — not idempotent.** |
 | `git_merge` | `rethunk-git_git_merge` | Merge one or more source branches into a destination. Default strategy `auto` cascades fast-forward → rebase → merge-commit per source, preferring linear history. Refuses on dirty tree; stops on first conflict with structured path report. Optional `deleteMergedBranches` / `deleteMergedWorktrees` cascade cleanup, always skipping protected names (main/master/dev/develop/stable/trunk/prod/production/release\*/hotfix\*). Args: `sources`, `into?`, `strategy?`, `message?`, cleanup flags + workspace pick + `format`. **Mutating.** |
-| `git_cherry_pick` | `rethunk-git_git_cherry_pick` | Play commits from one or more sources onto a destination. Sources may be SHAs, `A..B` ranges, or branch names (expanded to `onto..<branch>`, oldest-first). Uses `--empty=drop` so patch-equivalent re-applies add nothing. Refuses on dirty tree; stops on first conflict, aborting cleanly. Same cleanup flags as `git_merge` (branch-kind sources only, protected names skipped). Args: `sources`, `onto?`, cleanup flags + workspace pick + `format`. **Mutating.** |
+| `git_cherry_pick` | `rethunk-git_git_cherry_pick` | Play commits from one or more sources onto a destination. Sources may be SHAs, `A..B` ranges, or branch names (expanded to `onto..<branch>`, oldest-first). Uses `--empty=drop` so patch-equivalent re-applies add nothing. Refuses on dirty tree; stops on first conflict, aborting cleanly. Same cleanup flags as `git_merge` (branch-kind sources only, protected names skipped); branch deletion uses patch-id equivalence by default so cherry-pick workflows (where SHA differs but diff is identical) clean up correctly. Pass `strictMergedRefEquality: true` for strict `git branch -d` ancestry semantics. Args: `sources`, `onto?`, cleanup flags, `strictMergedRefEquality?` + workspace pick + `format`. **Mutating.** |
 | `git_stash_apply` | `rethunk-git_git_stash_apply` | Apply or pop a stash entry for one repo. Args: `index?`, `pop?`, plus single-repo workspace pick + `format`. **Mutating.** |
 
 Pass **`format: "json"`** on any tool for structured JSON instead of markdown (default).
 
+---
+
+### `git_status` — parameters
+
+| Parameter | Type | Default | Notes |
+|-----------|------|---------|-------|
+| `includeSubmodules` | boolean | `true` | When `true`, reads `.gitmodules` at each git toplevel and runs `git status --short -b` for each checked-out submodule in parallel. Set `false` to skip submodule discovery entirely. |
+| `workspaceRoot` | string | — | Explicit root; highest priority. |
+| `rootIndex` | int | — | Pick one of several MCP roots (0-based). |
+| `allWorkspaceRoots` | boolean | `false` | Fan out across all MCP roots. |
+| `absoluteGitRoots` | string[] | — | Explicit list of absolute paths; replaces normal workspace pick. Max 256. Read-only tools only. |
+| `format` | `"markdown"` \| `"json"` | `"markdown"` | Output format. |
+
+### `git_status` — JSON shape (`format: "json"`)
+
+```json
+{
+  "groups": [{
+    "mcpRoot": "/abs/workspace",
+    "repos": [
+      { "label": ".", "path": "/abs/workspace", "statusText": "## main...origin/main\nM src/foo.ts", "ok": true },
+      { "label": "sub", "path": "/abs/workspace/sub", "statusText": "## main...origin/main", "ok": true }
+    ]
+  }]
+}
+```
+
+One `groups` entry per resolved root. Each `repos` entry has `label` (relative path, `"."` for the root), `path` (absolute), `statusText` (full `git status --short -b` output), and `ok` (`false` when git failed or the submodule is not checked out).
+
+### `git_status` — error codes
+
+Error payloads appear as top-level JSON or inline in individual repo rows (`ok: false`):
+
+| Code / statusText | Context | Meaning |
+|-------------------|---------|---------|
+| `git_not_found` | top-level | `git` binary not on `PATH`. |
+| `not_a_git_repository` | repo row `statusText` | Root is not inside a git repository. |
+| `(submodule path escapes repository — rejected)` | repo row `statusText` | `.gitmodules` path resolves outside the git toplevel (security guard). |
+| `(no .git — submodule not checked out?)` | repo row `statusText` | Submodule directory exists but has no `.git` — not initialized. |
+| `root_index_out_of_range` | top-level | `rootIndex` exceeds the number of MCP file roots. |
+| `absolute_git_roots_exclusive` | top-level | `absoluteGitRoots` combined with `workspaceRoot`, `rootIndex`, or `allWorkspaceRoots: true`. |
+| `invalid_absolute_git_root` | top-level | An `absoluteGitRoots` entry is not a git-recognized directory. |
+| `absolute_git_roots_too_many` | top-level | More than 256 entries in `absoluteGitRoots`. |
+| `absolute_git_roots_empty` | top-level | `absoluteGitRoots` resolved to zero toplevels. |
+
+---
+
+### `git_inventory` — parameters
+
+| Parameter | Type | Default | Notes |
+|-----------|------|---------|-------|
+| `nestedRoots` | string[] | — | Relative paths (from the workspace git toplevel) to treat as independent git repos to inventory. Each must be a valid git work tree; invalid paths produce skip entries rather than errors. Cannot combine with `absoluteGitRoots` or `preset`. |
+| `preset` | string | — | Preset name from `.rethunk/git-mcp-presets.json`. Loads `nestedRoots` from the preset's entry. Cannot combine with `absoluteGitRoots`. |
+| `presetMerge` | boolean | `false` | When `true`, merge inline `nestedRoots` with preset roots instead of replacing. |
+| `remote` | string | — | Fixed remote for ahead/behind tracking. Must be paired with `branch`. |
+| `branch` | string | — | Fixed branch for ahead/behind tracking. Must be paired with `remote`. When both are absent the tool uses each repo's `@{u}` upstream. |
+| `maxRoots` | int | `64` | Max nested roots to process (1–256). Roots beyond the limit are omitted; `nestedRootsTruncated: true` and `nestedRootsOmittedCount` are set on the group. |
+| `workspaceRoot` | string | — | Explicit root; highest priority. |
+| `rootIndex` | int | — | Pick one of several MCP roots (0-based). |
+| `allWorkspaceRoots` | boolean | `false` | Fan out across all MCP roots. |
+| `absoluteGitRoots` | string[] | — | Explicit list; replaces normal workspace pick. Cannot combine with `nestedRoots` or `preset`. |
+| `format` | `"markdown"` \| `"json"` | `"markdown"` | Output format. |
+
+### `git_inventory` — JSON shape (`format: "json"`)
+
+```json
+{
+  "inventories": [{
+    "workspace_root": "/abs/path",
+    "entries": [{
+      "label": ".",
+      "path": "/abs/path",
+      "upstreamMode": "auto",
+      "branchStatus": "## main...origin/main",
+      "headAbbrev": "a1b2c3d",
+      "upstreamRef": "origin/main",
+      "ahead": "2",
+      "behind": "0"
+    }],
+    "nestedRootsTruncated": true,
+    "nestedRootsOmittedCount": 3,
+    "upstream": { "mode": "fixed", "remote": "origin", "branch": "main" }
+  }]
+}
+```
+
+`nestedRootsTruncated` / `nestedRootsOmittedCount` present only when `maxRoots` cut the list. `upstream` object present only when `remote`+`branch` were supplied (fixed mode). `presetSchemaVersion` present only when a preset was loaded. See *v2/v3 field omission* for `entries[*]` optional fields.
+
+### `git_inventory` — error codes
+
+| Code | Meaning |
+|------|---------|
+| `git_not_found` | `git` binary not on `PATH`. |
+| `remote_branch_mismatch` | Only one of `remote` / `branch` was provided; supply both or neither. |
+| `invalid_remote_or_branch` | `remote` or `branch` contains characters outside the safe token set. |
+| `absolute_git_roots_nested_or_preset_conflict` | `absoluteGitRoots` combined with `nestedRoots` or `preset`. |
+| `absolute_git_roots_exclusive` | `absoluteGitRoots` combined with `workspaceRoot`, `rootIndex`, or `allWorkspaceRoots: true`. |
+| `absolute_git_roots_preset_conflict` | `absoluteGitRoots` combined with a `preset` argument. |
+| `invalid_absolute_git_root` | An `absoluteGitRoots` entry is not a git-recognized directory. |
+| `absolute_git_roots_too_many` | More than 256 entries in `absoluteGitRoots`. |
+| `absolute_git_roots_empty` | `absoluteGitRoots` resolved to zero toplevels. |
+| `root_index_out_of_range` | `rootIndex` exceeds the number of MCP file roots. |
+| `preset_not_found` | Named preset does not exist in the preset file. |
+| `invalid_json` | Preset file contains invalid JSON. |
+| `invalid_schema` | Preset file fails schema validation. |
+
+Skip entries (individual repos that could not be inventoried) appear inline in `entries[*]` with `skipReason` rather than as top-level errors.
+
+---
+
+### `git_parity` — parameters
+
+| Parameter | Type | Notes |
+|-----------|------|-------|
+| `pairs` | `{left: string, right: string, label?: string}[]` | Path pairs to compare. `left` and `right` are relative to the workspace git toplevel. `label` is optional display name; defaults to `"left / right"`. At least one pair required (via inline `pairs` or `preset`). |
+| `preset` | string | Preset name from `.rethunk/git-mcp-presets.json`. Loads `parityPairs` from the preset's entry. |
+| `presetMerge` | boolean | Default `false`. When `true`, merge inline `pairs` with preset pairs instead of replacing. |
+| `workspaceRoot` | string | Explicit root; highest priority. |
+| `rootIndex` | int | Pick one of several MCP roots (0-based). |
+| `allWorkspaceRoots` | boolean | `false` | Fan out across all MCP roots. |
+| `absoluteGitRoots` | string[] | Explicit list of absolute paths; replaces normal workspace pick. Useful for checking parity across sibling clones. |
+| `format` | `"markdown"` \| `"json"` | Output format. Default: `"markdown"`. |
+
+### `git_parity` — JSON shape (`format: "json"`)
+
+```json
+{
+  "parity": [{
+    "workspace_root": "/abs/path",
+    "status": "MISMATCH",
+    "pairs": [
+      {
+        "label": "shared",
+        "leftPath": "/abs/path/left",
+        "rightPath": "/abs/path/right",
+        "match": true,
+        "sha": "a1b2c3d4e5f6…"
+      },
+      {
+        "label": "config",
+        "leftPath": "/abs/path/cfg-a",
+        "rightPath": "/abs/path/cfg-b",
+        "match": false,
+        "leftSha": "a1b2c3d…",
+        "rightSha": "f9e8d7c…"
+      }
+    ]
+  }]
+}
+```
+
+`status` is `"OK"` when every pair matches, `"MISMATCH"` when any pair differs or errors. On a match, `sha` carries the common HEAD SHA. On a mismatch, `leftSha` / `rightSha` carry the differing SHAs. On error (path escape or `git rev-parse HEAD` failure), `error` carries a description string and both SHA fields are absent. `presetSchemaVersion` is present when a preset was loaded.
+
+### `git_parity` — error codes
+
+| Code | Meaning |
+|------|---------|
+| `git_not_found` | `git` binary not on `PATH`. |
+| `no_pairs` | Neither inline `pairs` nor a preset with `parityPairs` was supplied. |
+| `absolute_git_roots_exclusive` | `absoluteGitRoots` combined with `workspaceRoot`, `rootIndex`, or `allWorkspaceRoots: true`. |
+| `absolute_git_roots_preset_conflict` | `absoluteGitRoots` combined with a `preset` argument. |
+| `invalid_absolute_git_root` | An `absoluteGitRoots` entry is not a git-recognized directory. |
+| `absolute_git_roots_too_many` | More than 256 entries in `absoluteGitRoots`. |
+| `absolute_git_roots_empty` | `absoluteGitRoots` resolved to zero toplevels. |
+| `root_index_out_of_range` | `rootIndex` exceeds the number of MCP file roots. |
+| `preset_not_found` | Named preset does not exist in the preset file. |
+| `invalid_json` | Preset file contains invalid JSON. |
+| `invalid_schema` | Preset file fails schema validation. |
+
+Path-escape and `rev-parse` failures are reported inline in `pairs[*].error`, not as top-level error codes.
+
+---
+
+### `list_presets` — parameters
+
+| Parameter | Type | Notes |
+|-----------|------|-------|
+| `workspaceRoot` | string | Explicit root; highest priority. |
+| `rootIndex` | int | Pick one of several MCP roots (0-based). |
+| `allWorkspaceRoots` | boolean | Default `false`. Fan out across all MCP roots. |
+| `absoluteGitRoots` | string[] | Explicit list; replaces normal workspace pick. |
+| `format` | `"markdown"` \| `"json"` | Output format. Default: `"markdown"`. |
+
+### `list_presets` — JSON shape (`format: "json"`)
+
+```json
+{
+  "roots": [{
+    "workspaceRoot": "/abs/workspace",
+    "gitTop": "/abs/workspace",
+    "presetFile": "/abs/workspace/.rethunk/git-mcp-presets.json",
+    "fileExists": true,
+    "presetSchemaVersion": "1",
+    "presets": [
+      {
+        "name": "monorepo",
+        "nestedRootsCount": 5,
+        "parityPairsCount": 2,
+        "workspaceRootHint": "/abs/workspace"
+      }
+    ]
+  }]
+}
+```
+
+`gitTop` is `null` when the workspace root is not inside a git repository. `presetSchemaVersion` is omitted when absent. `workspaceRootHint` is omitted when not set. When `fileExists: false` the `presets` array is empty and no `error` is present. When the file exists but fails to load, `error` contains a structured error object and `presets` is empty.
+
+### `list_presets` — error codes
+
+| Code | Meaning |
+|------|---------|
+| `git_not_found` | `git` binary not on `PATH`. |
+| `not_a_git_repository` | Root is not inside a git repository (reported inline in the `roots[*].error` field, not top-level). |
+| `invalid_json` | Preset file is not valid JSON (inline in `roots[*].error`). |
+| `invalid_schema` | Preset file fails schema validation (inline in `roots[*].error`). |
+| `absolute_git_roots_exclusive` | `absoluteGitRoots` combined with `workspaceRoot`, `rootIndex`, or `allWorkspaceRoots: true`. |
+| `invalid_absolute_git_root` | An `absoluteGitRoots` entry is not a git-recognized directory. |
+| `absolute_git_roots_too_many` | More than 256 entries in `absoluteGitRoots`. |
+| `absolute_git_roots_empty` | `absoluteGitRoots` resolved to zero toplevels. |
+| `root_index_out_of_range` | `rootIndex` exceeds the number of MCP file roots. |
+
+---
+
 ## JSON responses
 
-Tool JSON bodies are minified and contain only the payload — no `rethunkGitMcp` envelope. Current `MCP_JSON_FORMAT_VERSION` is **`"3"`**; server + format version are discoverable via MCP `initialize`. Payload keys (`groups`, `inventories`, `parity`, `roots`) are stable within a given format version. Preset-related responses may include **`presetSchemaVersion`**.
+Tool JSON bodies are minified and contain only the payload — no `rethunkGitMcp` envelope. Current `MCP_JSON_FORMAT_VERSION` is **`"3"`** (exported constant in `src/server.ts`); the version string is surfaced in the FastMCP `instructions` field and is therefore discoverable via the MCP `initialize` response. Payload keys (`groups`, `inventories`, `parity`, `roots`) are stable within a given format version. Preset-related responses may include **`presetSchemaVersion`**.
 
 The package also ships **`tool-parameters.schema.json`**, generated from the registered Zod parameter schemas via `bun run schema:tools`, plus the published **`schemas/`** directory (`schemas/index.json` + one JSON Schema per tool) via `bun run schema:individual`. Connected MCP clients should still prefer live schema discovery from `initialize` / tool listing; the shipped artifacts are for offline inspection, drift checks, and code generation.
 
@@ -59,7 +282,7 @@ To keep responses compact, **optional fields are omitted when they would be empt
 
 - Error payloads carry an `error` code string and any structured context (e.g. `preset`, `presetFile`). The old free-text `message` field is **removed** for self-describing codes (`git_not_found`, `remote_branch_mismatch`, `invalid_remote_or_branch`, `no_pairs`, `preset_not_found` *missing* case). It is retained only where it carries parse output (the `invalid_json` preset branch).
 
-**When to bump `MCP_JSON_FORMAT_VERSION` or change payload shape:** [AGENTS.md](../AGENTS.md) — *Changing contracts*.
+**When to bump `MCP_JSON_FORMAT_VERSION` or change payload shape:** [AGENTS.md](../AGENTS.md) — *Changing contracts*. The constant lives in `src/server.ts` and is surfaced via the server `instructions` field (discoverable from the MCP `initialize` response).
 
 ### `git_log` — parameters
 
@@ -74,7 +297,7 @@ To keep responses compact, **optional fields are omitted when they would be empt
 | `workspaceRoot` | string | — | Explicit root; highest priority. |
 | `rootIndex` | int | — | Pick one of several MCP roots (0-based). |
 | `allWorkspaceRoots` | boolean | `false` | Fan out across all MCP roots. |
-| `format` | `"markdown"` \| `"json"` | `"markdown"` | Output format. |
+| `format` | `"markdown"` \| `"json"` \| `"oneline"` | `"markdown"` | Output format. `oneline` returns `<sha7> <subject>` per line with no headers (single root) or `### repo (branch)` separators per group (multi-root). Lowest-token option for post-commit verification. |
 
 ### `git_log` — JSON shape (`format: "json"`)
 
@@ -112,6 +335,7 @@ v2 field-omission rules still apply: `filesChanged`, `insertions`, `deletions` o
 | `not_a_git_repository` | The resolved workspace root is not inside a git repository. |
 | `invalid_since` | The `since` string contains shell metacharacters and was rejected. |
 | `invalid_paths` | One of the `paths` entries contains shell metacharacters and was rejected. |
+| `unsafe_ref_token` | `branch` contains characters outside the argv-safe subset. |
 | `git_log_failed` | `git log` exited non-zero (e.g. unknown branch ref). |
 | `root_index_out_of_range` | `rootIndex` exceeds the number of MCP file roots. |
 | `absolute_git_roots_exclusive` | `absoluteGitRoots` was combined with `workspaceRoot`, `rootIndex`, or `allWorkspaceRoots: true`. |
@@ -193,7 +417,11 @@ The response contains one **`parity[]`** entry per resolved git toplevel. `absol
 | `head` | string | `HEAD` | Head ref for a revision diff. Used only when `base` is provided. |
 | `path` | string | — | Optional single file path to scope the diff. |
 | `staged` | boolean | `false` | When `true`, runs `git diff --staged`. Ignored when `base` is provided. |
-| `workspaceRoot`, `rootIndex`, `format` | — | Standard single-repo workspace pick + output format. |
+| `workspaceRoot` | string | — | Explicit root; highest priority. |
+| `rootIndex` | int | — | Pick one of several MCP roots (0-based). |
+| `format` | `"markdown"` \| `"json"` | `"markdown"` | Output format. |
+
+`git_diff` is a single-repo tool. It does not accept `absoluteGitRoots` or `allWorkspaceRoots`; use `workspaceRoot` or `rootIndex` to select the target repo.
 
 ### `git_diff` — JSON shape (`format: "json"`)
 
@@ -239,6 +467,8 @@ The response contains one **`parity[]`** entry per resolved git toplevel. `absol
 
 | Code | Meaning |
 |------|---------|
+| `unsafe_ref_token` | `ref` contains characters outside the argv-safe subset. |
+| `path_escapes_repo` | `path` resolves outside the git toplevel. |
 | `git_show_failed` | `git show` exited non-zero (e.g. unknown ref). |
 | `not_a_git_repository` | The resolved workspace root is not inside a git repository. |
 
@@ -297,6 +527,8 @@ Fetch failures are reported as `ok: false` with the captured git output in `outp
 
 | Code | Meaning |
 |------|---------|
+| `unsafe_remote_token` | `remote` contains characters outside the argv-safe subset. |
+| `unsafe_ref_token` | `branch` contains characters outside the argv-safe subset. |
 | `not_a_git_repository` | The resolved workspace root is not inside a git repository. |
 
 ---
@@ -327,7 +559,7 @@ Do NOT do this: make two separate calls hoping to stage files incrementally. Tha
 
 | Parameter | Type | Notes |
 |-----------|------|-------|
-| `commits` | `{message: string, files: (string \| {path: string, lines: {from: number, to: number}})[]}[]` | Commits to create in order. 1–50 entries. Each `files` entry is either a path relative to the git root or a `{path, lines}` object for hunk-level staging. All paths must stay within the git toplevel. |
+| `commits` | `{message: string, files: (string \| {path: string, lines: {from: number, to: number}})[]}[]` | Commits to create in order. 1–50 entries. Each `files` entry is either: (a) a path relative to the git root, staged with `git add`; (b) a `{path, lines: {from, to}}` object for hunk-level staging — only unified-diff hunks overlapping the given 1-indexed line range are staged; or (c) a path to a **deleted tracked file** (missing on disk but tracked in HEAD), which is staged as a removal via `git rm --cached` — combining `{path, lines}` with a deleted file is an error. All paths must stay within the git toplevel. |
 | `push` | `"never"` \| `"after"` | Default `"never"`. `"after"` pushes the current branch to its upstream **once all commits succeed**. Never auto-sets upstream — branches without an upstream fail with `push_no_upstream`. Commits are **not** rolled back on push failure. Enum reserved for future modes such as `"force-with-lease"`. |
 | `dryRun` | boolean | Default `false`. When `true`, stages each entry, reports what would be committed (`staged`, `diffStat`), then unstages everything without writing commits. |
 | `workspaceRoot` | string | Explicit root; highest priority. |
@@ -373,7 +605,7 @@ The `push` object is present only when `push: "after"` was requested **and** eve
 | Code | Meaning |
 |------|---------|
 | `path_escapes_repository` | One of the listed file paths resolves outside the git toplevel. |
-| `stage_failed` | `git add` failed (e.g. untracked path or permission error). |
+| `stage_failed` | Staging failed. `git add` error for modified/new files; `git rm --cached` error for deleted files (e.g. path never tracked in HEAD); `{path, lines}` on a deleted file. |
 | `commit_failed` | `git commit` failed (e.g. nothing staged, hooks rejected). |
 | `not_a_git_repository` | The resolved workspace root is not inside a git repository. |
 
@@ -457,8 +689,9 @@ On conflict: top-level `ok` is `false`, the conflicting entry has `ok: false` wi
 |-----------|------|-------|
 | `sources` | `string[]` | Source specs. 1–50 entries. Each entry is one of: a full/short SHA, an `A..B` / `A...B` range, or a branch name. Branch names expand to `onto..<branch>` (oldest-first). |
 | `onto` | string | Destination branch. Defaults to the currently checked-out branch. Rejected when HEAD is detached. |
-| `deleteMergedBranches` | boolean | Default `false`. After all commits apply, delete each **branch-kind** source locally (`git branch -d`) when it is fully merged into the destination by SHA-reachability (not patch-equivalence). Protected names always skipped; never touches remote refs. |
+| `deleteMergedBranches` | boolean | Default `false`. After all commits apply, delete each **branch-kind** source locally. Deletion uses **patch-id equivalence** by default — correct for cherry-pick workflows where SHA differs but diff is identical. Protected names always skipped; never touches remote refs. |
 | `deleteMergedWorktrees` | boolean | Default `false`. After success, remove any local worktree attached to a branch-kind source (`git worktree remove`). Protected tails always skipped. |
+| `strictMergedRefEquality` | boolean | Default `false`. When `true`, branch deletion uses strict SHA-reachability (`git branch -d` ancestry semantics) instead of patch-id equivalence. Use when you need git's exact ancestry guarantee rather than content equivalence. |
 | `workspaceRoot`, `rootIndex`, `format` | — | Standard workspace pick + output format. |
 
 ### `git_cherry_pick` — JSON shape (`format: "json"`)
@@ -568,9 +801,9 @@ For deletions, `type` is `"deleted"` and `sha` is an empty string.
 
 | Code | Meaning |
 |------|---------|
-| `tag_empty` | `tag` trimmed to an empty string. |
-| `tag_unsafe` | `tag` contains disallowed characters. |
-| `ref_unsafe` | `ref` contains disallowed characters. |
+| `empty_tag_name` | `tag` trimmed to an empty string. |
+| `unsafe_tag_token` | `tag` contains disallowed characters. |
+| `unsafe_ref_token` | `ref` contains disallowed characters. |
 | `ref_not_found` | `ref` did not resolve to a commit. |
 | `tag_create_failed` | `git tag` failed while creating the tag. |
 | `tag_delete_failed` | `git tag -d` failed. |

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rethunk/mcp-multi-root-git",
-  "version": "2.4.0",
+  "version": "2.6.0",
   "description": "MCP stdio server: multi-root git status, inventory, and HEAD parity checks. Generic tools usable by any workspace.",
   "type": "module",
   "private": false,
@@ -37,6 +37,7 @@
     "schema:tools": "bun scripts/generate-tool-parameters-schema.ts",
     "schema:tools:check": "bun scripts/generate-tool-parameters-schema.ts --check",
     "schema:individual": "bun scripts/generate-individual-schemas.ts",
+    "schema:individual:check": "bun scripts/generate-individual-schemas.ts --check",
     "publish:preflight": "bun scripts/publish-preflight.ts",
     "test": "bun test src/",
     "test:coverage": "bun test src/ --coverage",
@@ -68,9 +69,19 @@
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.14",
-    "@types/node": "^25.6.0",
+    "@biomejs/biome": "^2.4.15",
+    "@types/node": "^25.9.1",
     "rimraf": "^6.1.3",
     "typescript": "^6.0.3"
+  },
+  "overrides": {
+    "@hono/node-server": "^1.19.14",
+    "hono": "^4.12.18",
+    "fast-uri": "^3.1.2",
+    "postcss": "^8.5.10",
+    "vite": "^7.3.2",
+    "ip-address": "^10.1.1",
+    "axios": "^1.15.2",
+    "follow-redirects": "^1.15.12"
   }
 }

package/schemas/batch_commit.json

@@ -88,7 +88,7 @@
                 }
               ]
             },
-            "description": "Paths to stage, relative to the git root. Each can be a string path or { path, lines } for hunk-level staging."
+            "description": "Paths to stage, relative to the git root. Each can be a string path or { path, lines } for hunk-level staging. Deleted files (missing on disk but tracked in HEAD) are staged as removals via `git rm --cached`. Combining { path, lines } with a deleted file is an error."
           }
         },
         "required": [

package/schemas/git_cherry_pick.json

@@ -50,6 +50,11 @@
       "default": false,
       "description": "After success, remove any local worktree attached to a branch-kind source (`git worktree remove`). Protected tails always skipped.",
       "type": "boolean"
+    },
+    "strictMergedRefEquality": {
+      "default": false,
+      "description": "When false (default), branch deletion uses patch-id equivalence: a source branch is deleted when every commit it contains has a content-equivalent commit on the destination (same diff, different SHA — the normal cherry-pick outcome). Set to true to require strict ref ancestry (`git branch -d` semantics), which will refuse deletion after a cherry-pick because the SHA differs.",
+      "type": "boolean"
     }
   },
   "required": [
@@ -57,7 +62,8 @@
     "format",
     "sources",
     "deleteMergedBranches",
-    "deleteMergedWorktrees"
+    "deleteMergedWorktrees",
+    "strictMergedRefEquality"
   ],
   "additionalProperties": false
 }

package/schemas/git_diff.json

@@ -14,19 +14,6 @@
       "minimum": 0,
       "maximum": 9007199254740991
     },
-    "allWorkspaceRoots": {
-      "default": false,
-      "description": "Fan out across all MCP file roots.",
-      "type": "boolean"
-    },
-    "absoluteGitRoots": {
-      "description": "Absolute paths to git repo roots. Use for many sibling clones under a non-git parent directory.",
-      "maxItems": 256,
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
     "format": {
       "default": "markdown",
       "type": "string",
@@ -54,7 +41,6 @@
     }
   },
   "required": [
-    "allWorkspaceRoots",
     "format",
     "staged"
   ],

package/schemas/git_diff_summary.json

@@ -14,11 +14,6 @@
       "minimum": 0,
       "maximum": 9007199254740991
     },
-    "allWorkspaceRoots": {
-      "default": false,
-      "description": "Fan out across all MCP file roots.",
-      "type": "boolean"
-    },
     "absoluteGitRoots": {
       "description": "Absolute paths to git repo roots. Use for many sibling clones under a non-git parent directory.",
       "maxItems": 256,
@@ -66,7 +61,6 @@
     }
   },
   "required": [
-    "allWorkspaceRoots",
     "format",
     "maxLinesPerFile",
     "maxFiles"

package/schemas/git_log.json

@@ -29,10 +29,12 @@
     },
     "format": {
       "default": "markdown",
+      "description": "`markdown` (default): headed sections per root. `json`: structured groups array. `oneline`: `<sha7> <subject>` per line, no headers (single-root) or `### repo (branch)` separator per group (multi-root). Lowest-token option for post-commit verification.",
       "type": "string",
       "enum": [
         "markdown",
-        "json"
+        "json",
+        "oneline"
       ]
     },
     "since": {

package/schemas/git_show.json

@@ -24,6 +24,7 @@
     },
     "ref": {
       "type": "string",
+      "minLength": 1,
       "description": "Commit reference (SHA, branch, tag, or any git rev-spec)."
     },
     "path": {

package/tool-parameters.schema.json

@@ -266,10 +266,12 @@
         },
         "format": {
           "default": "markdown",
+          "description": "`markdown` (default): headed sections per root. `json`: structured groups array. `oneline`: `<sha7> <subject>` per line, no headers (single-root) or `### repo (branch)` separator per group (multi-root). Lowest-token option for post-commit verification.",
           "type": "string",
           "enum": [
             "markdown",
-            "json"
+            "json",
+            "oneline"
           ]
         },
         "since": {
@@ -324,11 +326,6 @@
           "minimum": 0,
           "maximum": 9007199254740991
         },
-        "allWorkspaceRoots": {
-          "default": false,
-          "description": "Fan out across all MCP file roots.",
-          "type": "boolean"
-        },
         "absoluteGitRoots": {
           "description": "Absolute paths to git repo roots. Use for many sibling clones under a non-git parent directory.",
           "maxItems": 256,
@@ -376,7 +373,6 @@
         }
       },
       "required": [
-        "allWorkspaceRoots",
         "format",
         "maxLinesPerFile",
         "maxFiles"
@@ -397,19 +393,6 @@
           "minimum": 0,
           "maximum": 9007199254740991
         },
-        "allWorkspaceRoots": {
-          "default": false,
-          "description": "Fan out across all MCP file roots.",
-          "type": "boolean"
-        },
-        "absoluteGitRoots": {
-          "description": "Absolute paths to git repo roots. Use for many sibling clones under a non-git parent directory.",
-          "maxItems": 256,
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
         "format": {
           "default": "markdown",
           "type": "string",
@@ -437,7 +420,6 @@
         }
       },
       "required": [
-        "allWorkspaceRoots",
         "format",
         "staged"
       ],
@@ -467,6 +449,7 @@
         },
         "ref": {
           "type": "string",
+          "minLength": 1,
           "description": "Commit reference (SHA, branch, tag, or any git rev-spec)."
         },
         "path": {
@@ -674,7 +657,7 @@
                     }
                   ]
                 },
-                "description": "Paths to stage, relative to the git root. Each can be a string path or { path, lines } for hunk-level staging."
+                "description": "Paths to stage, relative to the git root. Each can be a string path or { path, lines } for hunk-level staging. Deleted files (missing on disk but tracked in HEAD) are staged as removals via `git rm --cached`. Combining { path, lines } with a deleted file is an error."
               }
             },
             "required": [
@@ -884,6 +867,11 @@
           "default": false,
           "description": "After success, remove any local worktree attached to a branch-kind source (`git worktree remove`). Protected tails always skipped.",
           "type": "boolean"
+        },
+        "strictMergedRefEquality": {
+          "default": false,
+          "description": "When false (default), branch deletion uses patch-id equivalence: a source branch is deleted when every commit it contains has a content-equivalent commit on the destination (same diff, different SHA — the normal cherry-pick outcome). Set to true to require strict ref ancestry (`git branch -d` semantics), which will refuse deletion after a cherry-pick because the SHA differs.",
+          "type": "boolean"
         }
       },
       "required": [
@@ -891,7 +879,8 @@
         "format",
         "sources",
         "deleteMergedBranches",
-        "deleteMergedWorktrees"
+        "deleteMergedWorktrees",
+        "strictMergedRefEquality"
       ],
       "additionalProperties": false
     },