witan-code 0.23.0__tar.gz → 0.25.0__tar.gz

{witan_code-0.23.0 → witan_code-0.25.0}/.gitignore

@@ -26,7 +26,7 @@ build/
 *.egg-info/
 # omnigraph binary downloaded by hatch_build.py — not committed
 _bin/
-# omnigraph cluster state (populated by `omnigraph cluster import`)
+# omnigraph cluster state (populated by `omnigraph cluster apply`)
 __cluster/
 # The witan UI bundle, written by `npm run build` in mcp/servers/witan/ui/.
 # A build output, so not committed — hatch's `artifacts` setting in that

{witan_code-0.23.0 → witan_code-0.25.0}/CHANGELOG.md

@@ -8,6 +8,58 @@ a MINOR bump may include breaking changes).
 
 <!-- scriv-insert-here -->
 
+## [0.25.0] - 2026-10-15
+
+### Changed
+
+- `witan-code cleanup` no longer defaults to `--keep 10`. From omnigraph 0.12
+  `--keep` counts graph commits per live branch, not versions per table, so
+  that default would cut a store to its last ten writes. With neither bound
+  it now keeps the last 30 days, as the Stop hook does. The help text
+  describes both bounds in graph commits. `--older-than` on its own
+  no longer adds an implicit `--keep 10`.
+- The refusal for a shared cluster graph notes that from omnigraph 0.12
+  compaction is also refused while the server holds the cluster's `serve`
+  lock.
+
+- Requires witan-core 0.41 or later, the first release on omnigraph 0.13.
+  Every deployed omnigraph server is on 0.13 and refuses a client that does
+  not send `Omnigraph-Http-Api: 0.13`.
+
+### Fixed
+
+- `reap-views` ages a graph's views concurrently, `WITAN_CODE_VIEW_SURVEY_WORKERS` at a time (default 8; `1` is serial). Ageing a view is one `commit list --branch` that returns its whole reachable history, and serially production's 309-view bridge graph took 327s on its own, pushing the reaper CronJob past its 600s deadline; 8 workers take it to 50s. Each graph now also prints a `surveying views` line before its survey, so a job killed mid-sweep shows which graph it was on.
+
+- A cluster graph that is not served is recognised on omnigraph 0.13, whose
+  404 says `graph not found` without the quoted id. It was reported as an
+  unreachable cluster.
+
+## [0.24.0] - 2026-10-02
+
+### Added
+
+- `witan-code setup --force` replaces a symlink or non-directory occupying an install destination (e.g. a stale symlink under `~/.pi/agent/extensions`). Without it, `witan-code setup` now exits 2 with the conflicting path instead of a `FileNotFoundError` traceback.
+
+- `witan-code inject-context --client pi-builtin` renders the code-tool
+  discovery line for Pi's built-in MCP: a `codemode` script that finds the
+  `mcp__<server>__code_*` name with `searchTools()` and calls it as
+  `tools.<name>()`. The Pi extension passes it unless pi-mcp-adapter's `mcp`
+  tool is registered, in which case it still passes `--client pi`, whose
+  output is unchanged.
+
+### Changed
+
+- The `witan-code` skill describes calling the `code_*` tools under Pi's
+  built-in MCP as well as under pi-mcp-adapter, and `witan-code setup --agent
+  pi` no longer warns that pi-mcp-adapter is missing when Pi's built-in MCP
+  will read the witan-code entry.
+- Requires `agent-config-kit>=0.12`, which has that check; with an older one,
+  `witan-code setup --agent pi` still printed the pi-mcp-adapter warning.
+
+### Fixed
+
+- `witan-code checkpoint`'s background `optimize` now also runs `cleanup --older-than 30d` at most once per `WITAN_CODE_CLEANUP_INTERVAL` (default weekly; `0` disables). On omnigraph 0.11 `optimize` no longer reclaims the storage of branches deleted by `branches --prune` or `reap-views --apply`, and nothing ran `cleanup` unless done by hand. `witan-code optimize` gains `--cleanup-older-than` to run both in one process.
+
 ## [0.23.0] - 2026-09-28
 
 ### Added
@@ -353,7 +405,6 @@ a MINOR bump may include breaking changes).
   write threw". Deliberately still non-fatal — the per-repo index succeeds and
   is worth keeping — but "non-fatal" and "unreported" are different claims.
 
-
 - **The test suite no longer asserts an environment.** Four tests
   (`test_branches.py`'s three branch-view assertions and
   `test_graph.py::test_a_shared_branch_view_needs_an_identity_to_own_it`)

{witan_code-0.23.0 → witan_code-0.25.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: witan-code
-Version: 0.23.0
+Version: 0.25.0
 Summary: witan-code — tree-sitter code graph + cross-repo bridge (mounts under `witan code`)
 Project-URL: Homepage, https://github.com/mitodl/agent-kit/tree/main/mcp/servers/witan-code
 Project-URL: Repository, https://github.com/mitodl/agent-kit
@@ -10,7 +10,7 @@ License-Expression: BSD-3-Clause
 Keywords: agent,code-graph,coding-agent,mcp,static-analysis,tree-sitter
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.11
-Requires-Dist: agent-config-kit<1,>=0.10
+Requires-Dist: agent-config-kit<1,>=0.12
 Requires-Dist: cyclopts<6,>=4
 Requires-Dist: fastmcp<5,>=4
 Requires-Dist: joserfc<2,>=1.0
@@ -26,7 +26,7 @@ Requires-Dist: tree-sitter-sql<0.4,>=0.3
 Requires-Dist: tree-sitter-typescript<0.24,>=0.23
 Requires-Dist: tree-sitter-yaml<0.8,>=0.7
 Requires-Dist: tree-sitter<0.26,>=0.25
-Requires-Dist: witan-core[cli,observability,remote,sentry]<1,>=0.40
+Requires-Dist: witan-core[cli,observability,remote,sentry]<1,>=0.41
 Provides-Extra: tasks
 Requires-Dist: fastmcp-tasks<5,>=4; extra == 'tasks'
 Description-Content-Type: text/markdown
@@ -82,7 +82,7 @@ arbitration applies. See [`docs/BRANCH_INDEXING.md`](docs/BRANCH_INDEXING.md).
 The two layers compose through **soft symbol-ID references**. A Layer-1 node
 (e.g. a `lesson` or `agent_context`) can record symbol ids of the form:
 
-```
+```text
 repo#relative/path.py::QualifiedName
 e.g. https://github.com/mitodl/ol-django#app/svc.py::Service.run
 ```
@@ -299,11 +299,12 @@ witan-code setup --dry-run          # preview without writing
 witan-code setup --author "Jane Doe"  # attribution (default: git config user.name)
 ```
 
-On Pi, the MCP server entry (`~/.pi/agent/mcp.json`) is read only by the
-third-party pi-mcp-adapter Pi package, since Pi core has no MCP support:
-install it with `pi install npm:pi-mcp-adapter`, restart Pi, and confirm it
-in `pi list`. `witan-code setup --agent pi` warns when it cannot find the
-package declared in Pi's settings.
+On Pi, the MCP server entry (`~/.pi/agent/mcp.json`) is read by Pi's
+built-in MCP support (Pi 0.99 and later), or by the pi-mcp-adapter Pi
+package when that is installed; confirm with `pi mcp list` or `/mcp` inside
+Pi. `witan-code setup --agent pi` warns when Pi's settings show neither one
+would load it (the built-in turned off with `-builtin:mcp`, or a Pi older
+than 0.99, and no adapter declared).
 
 If `witan` is *also* installed and witan-code is importable in that same
 environment (e.g. via the `--with` in the `uv tool install`/MCP server's
@@ -354,6 +355,7 @@ symlink alternative:
 | `WITAN_AUTHOR` / `USER` | `unknown` | attribution string |
 | `WITAN_REPO` | — | override the detected repo slug |
 | `WITAN_CODE_OPTIMIZE_INTERVAL` | `86400` (daily) | throttle window (seconds) for `checkpoint`'s opportunistic store compaction; `0` disables it |
+| `WITAN_CODE_CLEANUP_INTERVAL` | `604800` (weekly) | throttle window (seconds) for the `cleanup --older-than 30d` that rides a `checkpoint` compaction; `0` disables it |
 | `WITAN_CODE_INDEX_ROLE` | `client` | `ci` designates this process the writer of a shared graph's default-branch view. Only meaningful against a shared cluster graph; local stores are unaffected. See [Branch indexing](docs/BRANCH_INDEXING.md#who-may-write-the-shared-default-branch-view) |
 | `WITAN_ACTOR` | derived from the `witan login` session | the identity that owns the branch views this process writes; an `act-…` id or a raw OIDC `sub`. For a non-interactive writer (CI, a maintenance job). See [Branch indexing](docs/BRANCH_INDEXING.md#per-writer-branch-views) |
 | `WITAN_CONFIG` | `~/.config/witan/config.toml` | config file path (see below) |
@@ -582,7 +584,9 @@ graph):
   instead.
 - `cleanup [--store PATH] [--bridge] [--keep N] [--older-than DUR] --yes` —
   reclaim disk by GC'ing old Lance versions (**destructive**; requires
-  `--yes`).
+  `--yes`). `--keep N` retains the newest N graph commits of every live
+  branch (omnigraph 0.12+; versions per table on 0.11); with neither bound it
+  keeps the last 30 days.
 - `checkpoint` — opportunistically compact the current repo's store and the
   bridge store if due (see [Hooks](#hooks)); registered as the `Stop` hook,
   not usually run by hand.
@@ -640,12 +644,18 @@ mechanisms keep this in check, mirroring that module (deliberately duplicated
 - **Opportunistic**: the `witan-code checkpoint` Stop hook spawns a
   throttled, detached `witan-code optimize` for the current repo's store and
   the shared bridge store, at most once per `WITAN_CODE_OPTIMIZE_INTERVAL`
-  (default daily; `0` disables) each — see [Hooks](#hooks).
-- **Scheduled**: `witan-code optimize [--store PATH | --bridge]` /
-  `witan-code cleanup --yes` for cron/systemd-timer driven maintenance on a
-  busy store. `optimize` is non-destructive and safe to run repeatedly;
-  `cleanup` GCs old Lance versions to reclaim disk and is destructive, so it
-  requires `--yes`.
+  (default daily; `0` disables) each — see [Hooks](#hooks). At most once per
+  `WITAN_CODE_CLEANUP_INTERVAL` (default weekly) the run also cleans up
+  versions older than 30 days. On omnigraph 0.11 that is the only thing that
+  reclaims the storage of branches deleted by `branches --prune` or
+  `reap-views --apply`; `optimize` no longer does.
+- **Scheduled**: `witan-code optimize [--store PATH | --bridge]
+  [--cleanup-older-than DURATION]` / `witan-code cleanup --yes` for
+  cron/systemd-timer driven maintenance on a busy store. `optimize` alone is
+  non-destructive and safe to run repeatedly. `cleanup` GCs old Lance versions
+  to reclaim disk and is destructive, so it requires `--yes`.
+  `--cleanup-older-than` makes `optimize` run that destructive cleanup
+  afterwards with no `--yes` prompt, which is how the Stop hook calls it.
 
 ## Rebuilding an unreadable store
 
@@ -721,10 +731,13 @@ A Pi equivalent of all four lives in one extension,
   can tell "no cross-repo consumers" from "no cross-repo data"), and the
   `ToolSearch` call that makes the `code_*` tools callable when the harness
   delivers them deferred — followed by a `code_find_definition` →
-  `code_callers`/`code_impact` call template. `--client pi` (what the Pi
-  extension passes) swaps the `ToolSearch` step for pi-mcp-adapter's `mcp`
-  proxy: `mcp({ search: ... })` for the exact server-prefixed name, then
-  `mcp({ tool: ..., args: {...} })`. The default stays Claude's.
+  `code_callers`/`code_impact` call template. The Pi extension swaps the
+  `ToolSearch` step for Pi's calling convention: `--client pi-builtin`, for
+  Pi's built-in MCP, gives a `codemode` script (`searchTools(...)` for the
+  exact `mcp__<server>__` name, then `tools.<name>({...})`), and
+  `--client pi`, which it passes when pi-mcp-adapter's `mcp` tool is
+  registered, gives the adapter's proxy (`mcp({ search: ... })`, then
+  `mcp({ tool: ..., args: {...} })`). The default stays Claude's.
   Independent of `witan`'s own `inject-context` hook (no cross-package
   coupling) — register it alone for a witan-code-only install. Prints
   nothing when the repo has neither a store nor an index in flight.

{witan_code-0.23.0 → witan_code-0.25.0}/README.md

@@ -49,7 +49,7 @@ arbitration applies. See [`docs/BRANCH_INDEXING.md`](docs/BRANCH_INDEXING.md).
 The two layers compose through **soft symbol-ID references**. A Layer-1 node
 (e.g. a `lesson` or `agent_context`) can record symbol ids of the form:
 
-```
+```text
 repo#relative/path.py::QualifiedName
 e.g. https://github.com/mitodl/ol-django#app/svc.py::Service.run
 ```
@@ -266,11 +266,12 @@ witan-code setup --dry-run          # preview without writing
 witan-code setup --author "Jane Doe"  # attribution (default: git config user.name)
 ```
 
-On Pi, the MCP server entry (`~/.pi/agent/mcp.json`) is read only by the
-third-party pi-mcp-adapter Pi package, since Pi core has no MCP support:
-install it with `pi install npm:pi-mcp-adapter`, restart Pi, and confirm it
-in `pi list`. `witan-code setup --agent pi` warns when it cannot find the
-package declared in Pi's settings.
+On Pi, the MCP server entry (`~/.pi/agent/mcp.json`) is read by Pi's
+built-in MCP support (Pi 0.99 and later), or by the pi-mcp-adapter Pi
+package when that is installed; confirm with `pi mcp list` or `/mcp` inside
+Pi. `witan-code setup --agent pi` warns when Pi's settings show neither one
+would load it (the built-in turned off with `-builtin:mcp`, or a Pi older
+than 0.99, and no adapter declared).
 
 If `witan` is *also* installed and witan-code is importable in that same
 environment (e.g. via the `--with` in the `uv tool install`/MCP server's
@@ -321,6 +322,7 @@ symlink alternative:
 | `WITAN_AUTHOR` / `USER` | `unknown` | attribution string |
 | `WITAN_REPO` | — | override the detected repo slug |
 | `WITAN_CODE_OPTIMIZE_INTERVAL` | `86400` (daily) | throttle window (seconds) for `checkpoint`'s opportunistic store compaction; `0` disables it |
+| `WITAN_CODE_CLEANUP_INTERVAL` | `604800` (weekly) | throttle window (seconds) for the `cleanup --older-than 30d` that rides a `checkpoint` compaction; `0` disables it |
 | `WITAN_CODE_INDEX_ROLE` | `client` | `ci` designates this process the writer of a shared graph's default-branch view. Only meaningful against a shared cluster graph; local stores are unaffected. See [Branch indexing](docs/BRANCH_INDEXING.md#who-may-write-the-shared-default-branch-view) |
 | `WITAN_ACTOR` | derived from the `witan login` session | the identity that owns the branch views this process writes; an `act-…` id or a raw OIDC `sub`. For a non-interactive writer (CI, a maintenance job). See [Branch indexing](docs/BRANCH_INDEXING.md#per-writer-branch-views) |
 | `WITAN_CONFIG` | `~/.config/witan/config.toml` | config file path (see below) |
@@ -549,7 +551,9 @@ graph):
   instead.
 - `cleanup [--store PATH] [--bridge] [--keep N] [--older-than DUR] --yes` —
   reclaim disk by GC'ing old Lance versions (**destructive**; requires
-  `--yes`).
+  `--yes`). `--keep N` retains the newest N graph commits of every live
+  branch (omnigraph 0.12+; versions per table on 0.11); with neither bound it
+  keeps the last 30 days.
 - `checkpoint` — opportunistically compact the current repo's store and the
   bridge store if due (see [Hooks](#hooks)); registered as the `Stop` hook,
   not usually run by hand.
@@ -607,12 +611,18 @@ mechanisms keep this in check, mirroring that module (deliberately duplicated
 - **Opportunistic**: the `witan-code checkpoint` Stop hook spawns a
   throttled, detached `witan-code optimize` for the current repo's store and
   the shared bridge store, at most once per `WITAN_CODE_OPTIMIZE_INTERVAL`
-  (default daily; `0` disables) each — see [Hooks](#hooks).
-- **Scheduled**: `witan-code optimize [--store PATH | --bridge]` /
-  `witan-code cleanup --yes` for cron/systemd-timer driven maintenance on a
-  busy store. `optimize` is non-destructive and safe to run repeatedly;
-  `cleanup` GCs old Lance versions to reclaim disk and is destructive, so it
-  requires `--yes`.
+  (default daily; `0` disables) each — see [Hooks](#hooks). At most once per
+  `WITAN_CODE_CLEANUP_INTERVAL` (default weekly) the run also cleans up
+  versions older than 30 days. On omnigraph 0.11 that is the only thing that
+  reclaims the storage of branches deleted by `branches --prune` or
+  `reap-views --apply`; `optimize` no longer does.
+- **Scheduled**: `witan-code optimize [--store PATH | --bridge]
+  [--cleanup-older-than DURATION]` / `witan-code cleanup --yes` for
+  cron/systemd-timer driven maintenance on a busy store. `optimize` alone is
+  non-destructive and safe to run repeatedly. `cleanup` GCs old Lance versions
+  to reclaim disk and is destructive, so it requires `--yes`.
+  `--cleanup-older-than` makes `optimize` run that destructive cleanup
+  afterwards with no `--yes` prompt, which is how the Stop hook calls it.
 
 ## Rebuilding an unreadable store
 
@@ -688,10 +698,13 @@ A Pi equivalent of all four lives in one extension,
   can tell "no cross-repo consumers" from "no cross-repo data"), and the
   `ToolSearch` call that makes the `code_*` tools callable when the harness
   delivers them deferred — followed by a `code_find_definition` →
-  `code_callers`/`code_impact` call template. `--client pi` (what the Pi
-  extension passes) swaps the `ToolSearch` step for pi-mcp-adapter's `mcp`
-  proxy: `mcp({ search: ... })` for the exact server-prefixed name, then
-  `mcp({ tool: ..., args: {...} })`. The default stays Claude's.
+  `code_callers`/`code_impact` call template. The Pi extension swaps the
+  `ToolSearch` step for Pi's calling convention: `--client pi-builtin`, for
+  Pi's built-in MCP, gives a `codemode` script (`searchTools(...)` for the
+  exact `mcp__<server>__` name, then `tools.<name>({...})`), and
+  `--client pi`, which it passes when pi-mcp-adapter's `mcp` tool is
+  registered, gives the adapter's proxy (`mcp({ search: ... })`, then
+  `mcp({ tool: ..., args: {...} })`). The default stays Claude's.
   Independent of `witan`'s own `inject-context` hook (no cross-package
   coupling) — register it alone for a witan-code-only install. Prints
   nothing when the repo has neither a store nor an index in flight.

{witan_code-0.23.0 → witan_code-0.25.0}/docs/BRANCH_INDEXING.md

@@ -222,6 +222,8 @@ date, owner, or size. Two rules follow:
   ago — reaping it would race the indexer that just created it.
 
 The window is `WITAN_CODE_VIEW_MAX_IDLE_DAYS` (default 14; `0` disables).
+Ageing a view is one `commit list` per view, so the sweep ages
+`WITAN_CODE_VIEW_SURVEY_WORKERS` views at once (default 8; `1` is serial).
 Idleness is not abandonment: a branch parked past the window and picked back up
 loses its view, not its work, and the next index rebuilds it. Reporting is the
 default and `--apply` deletes, because the window is the one input nothing

{witan_code-0.23.0 → witan_code-0.25.0}/docs/PACKAGE_MAP.md

@@ -80,7 +80,7 @@ only makes it authoritative.
 One `PackageMap` node per repo in the bridge store, keyed on the repo URI and
 overwritten on every full-repo index (merge-by-slug):
 
-```
+```text
 node PackageMap {
     slug: String @key      // canonical repo URI
     repo: String @index

{witan_code-0.23.0 → witan_code-0.25.0}/docs/SYMBOL_FORMAT.md

@@ -13,7 +13,7 @@ the `:CALLS/heuristic` fallback.
 
 ## Format
 
-```
+```text
 {scheme}:{manager}:{package}:{version}:{descriptor}
 ```
 
@@ -35,7 +35,7 @@ never encoded (they are terminal).
 
 ### `endpoint` → scheme `http`
 
-```
+```text
 {METHOD} {normalized-path}
 ```
 
@@ -49,7 +49,7 @@ never encoded (they are terminal).
   representation, not the resource, and no consumer/provider pair would agree
   on them syntactically.
 
-```
+```text
 provider:  http:pypi:mit-learn:main:GET /api/v0/users/me
 consumer:  http:.:.:.:* /api/v0/users/me
 ```
@@ -58,7 +58,7 @@ consumer:  http:.:.:.:* /api/v0/users/me
 
 Descriptor is the variable name, verbatim.
 
-```
+```text
 provider:  env:.:mit-learn:main:MITOL_APP_BASE_URL
 consumer:  env:.:.:.:MITOL_APP_BASE_URL
 ```
@@ -69,7 +69,7 @@ The symbol identifies the package itself; the descriptor is `.`. Manager and
 package name come from the import site (consumer) or the publishing repo's
 package map / `package.json` (provider).
 
-```
+```text
 provider:  pkg:npm:@mitodl/course-search-utils:main:.
 consumer:  pkg:npm:@mitodl/course-search-utils:.:.
 ```
@@ -78,7 +78,7 @@ consumer:  pkg:npm:@mitodl/course-search-utils:.:.
 
 Descriptor is `{sub_kind}/{key_norm}` (sub_kind: `repo` | `image` | `name`).
 
-```
+```text
 provider:  svc:.:ol-infrastructure:main:repo/https://github.com/mitodl/mit-learn
 ```
 

{witan_code-0.23.0 → witan_code-0.25.0}/docs/SYMBOL_TABLE.md

@@ -93,7 +93,7 @@ bridge store predates `RepoSymbol` — the write is never blocked on it.
 
 ## Inspecting
 
-```
+```text
 witan code symbols [--repo URI] [--role exported|external] [--scheme http]
 witan code stitch [--repo URI] [--unresolved]
 ```

{witan_code-0.23.0 → witan_code-0.25.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "witan-code"
-version = "0.23.0"
+version = "0.25.0"
 description = "witan-code — tree-sitter code graph + cross-repo bridge (mounts under `witan code`)"
 readme = "README.md"
 license = "BSD-3-Clause"
@@ -18,10 +18,19 @@ dependencies = [
     # agent-config-kit by path — except there is NO `check-core-floor`
     # equivalent for this dependency, so this line is the only guard.
     # >=0.10: `witan-code setup`'s install report promises a warning when Pi
-    # lacks pi-mcp-adapter, which comes from `InstallResult.prerequisites`,
+    # cannot load MCP servers, which comes from `InstallResult.prerequisites`,
     # added in 0.10.0. witan_core's `report_install` reads it with getattr, so
     # an older resolution does not fail — it just silently drops the warning.
-    "agent-config-kit>=0.10,<1",
+    # >=0.11.1: `setup --force` passes `force` through to apply(), whose
+    # symlink guard (ConflictingPathError instead of FileNotFoundError) is
+    # new in 0.11.1. Older resolutions accept the flag but still crash on a
+    # dangling symlink. The workspace resolves by path, so no test here
+    # catches a stale floor.
+    # >=0.12: `witan-code setup --agent pi` only stops warning that
+    # pi-mcp-adapter is missing when Pi's built-in MCP will load the entry
+    # from 0.12.0. Older resolutions import and run, and print the false
+    # warning.
+    "agent-config-kit>=0.12,<1",
     # `remote`: the ADR-0005 client stack (OIDC device grant + MCP-client
     # proxy) behind `witan-code login` and the read commands' remote mode.
     # Costs nothing extra in practice — fastmcp is already required here and
@@ -157,11 +166,17 @@ dependencies = [
     # 0.38 its text never reaches the `mcp.tool_call` log line.
     #
     # ★ >=0.40 IS A BEHAVIOUR FLOOR too: `witan-code setup --agent pi` promises
-    # a warning when Pi lacks pi-mcp-adapter, and
+    # a warning when Pi cannot load MCP servers, and
     # `witan_core.cli.report_install` only prints `InstallResult.prerequisites`
     # from 0.40.0. It reads the field with getattr, so 0.39 imports and runs —
     # and silently drops the warning.
-    "witan-core[cli,remote,observability,sentry]>=0.40,<1",
+    #
+    # ★ >=0.41 IS A COMPATIBILITY FLOOR: 0.41.0 pins omnigraph 0.13 (storage
+    # format 14) and sends `Omnigraph-Http-Api: 0.13`. Every deployed server
+    # is on 0.13, which answers a request without that header with `400
+    # api_contract_mismatch`, so 0.40 imports and runs, then fails on the
+    # first read of a shared code graph.
+    "witan-core[cli,remote,observability,sentry]>=0.41,<1",
     "fastmcp>=4,<5",
     "cyclopts>=4,<6",
     # [targets.<name>] override models (config.py) — also transitively pulled
@@ -244,7 +259,7 @@ testpaths = ["tests"]
 packages = ["witan_code"]
 
 [tool.bumpversion]
-current_version = "0.23.0"
+current_version = "0.25.0"
 allow_dirty = true
 
 [[tool.bumpversion.files]]

{witan_code-0.23.0 → witan_code-0.25.0}/tests/test_cli_hooks.py

@@ -5,6 +5,8 @@ exception escape (the hooks are documented as "always exits 0"), and must
 not print an extra trailing newline beyond what the backend already returns.
 """
 
+import pytest
+
 from witan_code import cli
 
 
@@ -62,7 +64,8 @@ def test_inject_context_cmd_defaults_to_the_claude_client(monkeypatch, capsys):
     assert seen == ["claude"]
 
 
-def test_inject_context_cmd_passes_an_explicit_pi_client_through(monkeypatch):
+@pytest.mark.parametrize("client", ["pi", "pi-builtin"])
+def test_inject_context_cmd_passes_an_explicit_pi_client_through(monkeypatch, client):
     import witan_code.context as context_module
 
     seen = []
@@ -70,7 +73,7 @@ def test_inject_context_cmd_passes_an_explicit_pi_client_through(monkeypatch):
         context_module, "inject_context", lambda client: seen.append(client) or ""
     )
 
-    command, bound, _ = cli.app.parse_args(["inject-context", "--client", "pi"])
+    command, bound, _ = cli.app.parse_args(["inject-context", "--client", client])
     command(*bound.args, **bound.kwargs)
 
-    assert seen == ["pi"]
+    assert seen == [client]

{witan_code-0.23.0 → witan_code-0.25.0}/tests/test_context.py

@@ -417,10 +417,31 @@ def test_inject_context_default_and_explicit_claude_render_the_same(
     assert "`/witan-code`" in default
 
 
+def test_inject_context_for_pi_builtin_names_a_codemode_script(tmp_path, monkeypatch):
+    """Pi's built-in MCP declares no MCP tool to the model by default: a
+    `codemode` script finds them with `searchTools()` and calls them as
+    `tools.<name>()`. The `mcp__<server>__` prefix depends on the user's
+    config, so the block must search first and then call the returned name.
+    """
+    _indexed(tmp_path, monkeypatch)
+
+    text = context.inject_context(client="pi-builtin")
+
+    assert "ToolSearch" not in text
+    assert "mcp({" not in text
+    assert "`codemode` script" in text
+    assert 'return await searchTools("code_find_definition callers impact")' in text
+    assert 'return await tools.<name the search returned>({ name: "X" })' in text
+    assert "/skill:witan-code" in text
+    # The status lines above the discovery line are client-neutral.
+    assert "https://github.com/test/cg" in text
+    assert "3 files" in text
+
+
 def test_inject_context_for_pi_names_the_mcp_proxy_not_toolsearch(
     tmp_path, monkeypatch
 ):
-    """Pi has no ToolSearch; its MCP tools sit behind pi-mcp-adapter's `mcp`.
+    """With pi-mcp-adapter (`--client pi`), MCP tools sit behind its `mcp`.
 
     The adapter prefixes each tool with its server name, and that prefix
     depends on the user's config, so the block must search first and then

{witan_code-0.23.0 → witan_code-0.25.0}/tests/test_maintenance.py

@@ -70,16 +70,70 @@ def test_spawn_background_optimize_throttles(monkeypatch, tmp_path):
     monkeypatch.setattr(maintenance.subprocess, "Popen", _FakePopen)
 
     # first call spawns and stamps; second (within window) is throttled
-    assert maintenance.spawn_background_optimize(store, now=50_000.0) is True
-    assert maintenance.spawn_background_optimize(store, now=50_000.0 + 5) is False
+    assert maintenance.spawn_background_optimize(store, now=1_000_000.0) is True
+    assert maintenance.spawn_background_optimize(store, now=1_000_000.0 + 5) is False
     assert len(calls) == 1
     argv, kwargs = calls[0]
-    assert argv[1:] == ["-m", "witan_code", "optimize", "--store", str(store)]
+    # never cleaned up before, so the first run also cleans up
+    assert argv[1:] == [
+        "-m",
+        "witan_code",
+        "optimize",
+        "--store",
+        str(store),
+        "--cleanup-older-than",
+        maintenance.CLEANUP_OLDER_THAN,
+    ]
     assert kwargs["start_new_session"] is True
 
-    # after the window elapses it spawns again
-    assert maintenance.spawn_background_optimize(store, now=50_000.0 + 4000) is True
+    # after the optimize window elapses it spawns again, without the cleanup,
+    # whose weekly window has not
+    assert maintenance.spawn_background_optimize(store, now=1_000_000.0 + 4000) is True
     assert len(calls) == 2
+    assert "--cleanup-older-than" not in calls[1][0]
+
+
+def test_cleanup_rides_optimize_on_its_own_window(monkeypatch, tmp_path):
+    """omnigraph 0.11 reclaims deleted branches' storage only in `cleanup`, so
+    the throttled optimize has to run one now and then or local stores grow
+    without bound."""
+    from witan_code import maintenance
+
+    monkeypatch.setenv("TMPDIR", str(tmp_path))
+    monkeypatch.setenv("WITAN_CODE_OPTIMIZE_INTERVAL", "3600")
+    monkeypatch.setenv("WITAN_CODE_CLEANUP_INTERVAL", "86400")
+    store = tmp_path / "g.omni"
+    store.mkdir()
+
+    calls = []
+    monkeypatch.setattr(
+        maintenance.subprocess, "Popen", lambda argv, **kw: calls.append(argv)
+    )
+
+    for hour in range(26):
+        maintenance.spawn_background_optimize(store, now=100_000.0 + hour * 3600)
+    cleaned = ["--cleanup-older-than" in argv for argv in calls]
+    assert len(calls) == 26
+    assert cleaned.count(True) == 2
+    assert cleaned[0] and cleaned[24]
+
+
+def test_cleanup_disabled_leaves_optimize_alone(monkeypatch, tmp_path):
+    from witan_code import maintenance
+
+    monkeypatch.setenv("TMPDIR", str(tmp_path))
+    monkeypatch.setenv("WITAN_CODE_OPTIMIZE_INTERVAL", "3600")
+    monkeypatch.setenv("WITAN_CODE_CLEANUP_INTERVAL", "0")
+    store = tmp_path / "g.omni"
+    store.mkdir()
+
+    calls = []
+    monkeypatch.setattr(
+        maintenance.subprocess, "Popen", lambda argv, **kw: calls.append(argv)
+    )
+
+    assert maintenance.spawn_background_optimize(store, now=50_000.0) is True
+    assert "--cleanup-older-than" not in calls[0]
 
 
 def test_spawn_marks_before_spawn_so_failure_does_not_hotloop(monkeypatch, tmp_path):
@@ -177,6 +231,47 @@ def test_cli_optimize_and_cleanup(tmp_path, capsys):
     assert "Cleaned up" in capsys.readouterr().out
 
 
+def test_cli_cleanup_with_no_bound_keeps_the_hooks_window(
+    tmp_path, capsys, monkeypatch
+):
+    """From omnigraph 0.12 `--keep` counts graph commits, so a default of
+    `--keep 10` would cut a store to its last ten writes. No bound means the
+    age window the Stop hook already uses."""
+    from witan_code import cli as cli_module
+    from witan_code import maintenance
+
+    store = tmp_path / "s.omni"
+    store.mkdir()
+    calls = []
+
+    class _Client:
+        def cleanup(self, **kwargs):
+            calls.append(kwargs)
+
+    monkeypatch.setattr(cli_module, "_maintenance_client", lambda _ref: _Client())
+
+    cli_module.cleanup(store=str(store))
+    assert f"newer than {maintenance.CLEANUP_OLDER_THAN}" in capsys.readouterr().out
+    assert calls == []
+
+    cli_module.cleanup(store=str(store), yes=True)
+    cli_module.cleanup(store=str(store), keep=3, yes=True)
+    assert calls == [
+        {"keep": None, "older_than": maintenance.CLEANUP_OLDER_THAN},
+        {"keep": 3, "older_than": None},
+    ]
+
+
+@requires_omnigraph
+def test_cli_optimize_then_cleanup(tmp_path, capsys):
+    from witan_code import cli as cli_module
+
+    store = _fresh_store(tmp_path)
+
+    cli_module.optimize(store=str(store), cleanup_older_than="30d")
+    assert "Optimized and cleaned up" in capsys.readouterr().out
+
+
 def test_cli_optimize_missing_store_is_noop(tmp_path, capsys):
     from witan_code import cli as cli_module