Changelog

0.3.40 — 2026-05-29

Added — server::watch default skip-patterns

The watch primitive now drops events under conventional noise paths (.git/, target/, node_modules/, __pycache__/, .venv/, build/, dist/, .DS_Store) and noise extensions (.pyc, .pyo, .swp, .swo, .tmp) before the debounced callback runs. A wide-sandbox watcher under active development can generate hundreds of FSEvents per second from cargo build / npm install / git operations alone; without the filter every consumer either rebuilt wastefully or implemented the same skip list. With it, consumers see only events that could plausibly matter.

New API:

pub const DEFAULT_SKIP_SUBSTRINGS: &[&str] = &[
    "/.git/", "/target/", "/node_modules/", "/__pycache__/",
    "/.venv/", "/build/", "/dist/", "/.DS_Store",
];
pub const DEFAULT_SKIP_EXTENSIONS: &[&str] = &[
    "pyc", "pyo", "swp", "swo", "tmp",
];

pub struct WatchConfig {
    pub skip_substrings: Vec<String>,
    pub skip_extensions: Vec<String>,
}
impl WatchConfig {
    pub fn default() -> Self;     // recommended; uses the DEFAULT_* sets above
    pub fn unfiltered() -> Self;  // empty skip set; every event reaches the callback
    pub fn is_skipped(&self, path: &Path) -> bool;
}

pub fn watch_with_config(
    dir: &Path,
    on_change: Option<ChangeHandler>,
    debounce: Option<Duration>,
    config: WatchConfig,
) -> Result<WatchHandle>;

The existing pub fn watch(dir, on_change, debounce) is unchanged at the signature level; internally it now delegates to watch_with_config(..., WatchConfig::default()). Consumers that want every event opt out via watch_with_config(..., WatchConfig::unfiltered()).

Skip-substring matching is anchored with / on both sides where appropriate so a file literally named target at the repo root doesn’t false-match (but /repo/target/foo does). Matching is allocation-free per event. Empty post-filter batches (a pure-noise storm) skip the callback invocation entirely.

Why now

Originally surfaced by an MCP-servers operator deploying kglite-mcp-server with a wide workspace.root (/Volumes/EksternalHome/Koding, ~360k files). The cargo build storm under that root generated ~120 FSEvents/sec; the downstream kglite watch callback rebuilt the active code-tree on every event. kglite shipped its own fix on 2026-05-25 (active-root scoping + language_for_path filter + deferred rebuild — kglite main commits 6596da6 + 0306655), but the upstream server::watch is still walking those events through the FFI / debouncer cycle before the kglite filter drops them.

This change moves the skip to the source. Every server::watch consumer benefits — kglite’s filter becomes defense-in-depth, any future code-indexer-shaped consumer gets correct defaults, and the mcp-methods binary’s own log-changes mode emits fewer noise lines.

Compatibility

Existing callers see strictly fewer callback invocations for paths under the skip set. Any consumer relying on .git/objects/ writes hitting their callback has a bug already. No changes to watch(dir, on_change, debounce)’s signature; downstream kglite needs no source change to adopt — just bumps its mcp-methods pin when 0.3.40 ships.

Unit tests cover the default skip set, the unfiltered escape hatch, custom skip configs, anchoring (target file vs target/ dir), a positive end-to-end “callback fires on a real file change” test, and the debouncer’s batch-retention decision (retain_unskipped) — a noise-only batch retains nothing (so no callback fires), a mixed batch keeps only non-noise paths. The retention decision is tested as a pure function rather than against a live watcher, since inotify (Linux) and FSEvents (macOS) report different event paths for the same writes.

Fixed — graph_overview against kglite 0.10

fastmcp.register_overview forwarded a limit= kwarg to graph.describe(), which kglite dropped from KnowledgeGraph.describe() in the 0.10 line. Every graph_overview() call against a kglite ≥ 0.10 graph raised TypeError: describe() got an unexpected keyword argument 'limit' — a broken first-reach escape-hatch tool for any consumer on the current kglite. The limit parameter is removed; describe() already adapts its output to graph scale, so no replacement knob is needed. The test/example graph stubs now mirror the post-0.10 describe(types, connections) signature, so a regression that re-introduces limit forwarding fails the suite instead of passing against an over-permissive mock. Reported by kglite-docs (kglite 0.10.5, mcp-methods 0.3.39).

Fixed — cypher_query text mode returns a non-string

fastmcp.register_cypher_query returned graph.cypher(query) raw in text mode. kglite’s cypher() returns a lazy ResultView (Polars-backed, not a str), so the -> str tool handed a non-string to FastMCP’s output validation and the call failed. The text path now coerces with str() — ResultView.__str__ renders the result table — matching the defensive coercion the CSV path already did. Graph impls that already return a str pass through unchanged. Flagged by kglite-docs alongside the graph_overview report.

0.3.39 — 2026-05-22

Fixed — git_api doubled /repos/ for leading-slash paths

git_api_internal decided pass-through-vs-prefix by testing the path against a top_level list (repos/, search/, …) whose entries have no leading slash. A path written in the idiomatic absolute form the GitHub REST docs render — /repos/owner/name, /search/issues?q=… — matched none of them, fell into the relative branch, and got wrapped in /repos/<repo>/, producing a doubled prefix and a 404:

git_api("someorg/somerepo", "/repos/kkollsga/kglite")
  actual: https://api.github.com/repos/someorg/somerepo//repos/kkollsga/kglite → 404
  want:   https://api.github.com/repos/kkollsga/kglite

The same call without the leading slash worked, which made the failure surprising and slow to diagnose. URL construction now strips a single leading slash before the top_level check, so /repos/… and repos/… (and /search/… vs search/…) are equivalent.

Reported by kglite (their issue #19), surfaced through kglite’s github_api MCP tool against non-active repos.

Changed — URL construction lifted into build_git_api_url

The pure URL-building logic is now a build_git_api_url(repo, path) helper that git_api_internal calls, so a regression test can assert on the constructed URL without a network round-trip — a URL-building bug with no unit coverage is the kind that silently comes back.

Tests

• leading_slash_paths_normalise — leading and non-leading slash forms build the same URL for both top-level and relative paths.

0.3.38 — 2026-05-18

Added — Registry::from_manifest on the Rust crate

The one-shot manifest → resolved-skills-registry orchestration that previously lived only in mcp-methods-py’s SkillRegistry.from_manifest is now a public method on the Rust Registry builder:

let registry = mcp_methods::server::Registry::from_manifest(&manifest_path, true)?;

Loads the manifest, optionally merges framework bundled defaults, auto-detects the project layer at <basename>.skills/, layers in operator-declared skills: paths, and finalises in a single call. Use the builder directly for bespoke layering (e.g. supplying a SkillPredicateEvaluator via with_predicate_evaluator, or include_str!’d downstream bundled skills via add_bundled).

The pyo3 wheel’s SkillRegistry.from_manifest now delegates to this method — no public Python API change. Downstream pyo3 wrappers that consume mcp-methods from crates.io (kglite’s incoming kglite._mcp_internal wrapper crate, others) can now call the same library function instead of replicating the six-line orchestration, eliminating drift risk on future layering tweaks.

Added — SkillError::Manifest variant

Carries the manifest path + message when from_manifest fails at the manifest-load step (before any skill loading happens). Lets callers distinguish “your YAML is broken” from “your skills/ tree is broken” without parsing error messages.

Motivated by kglite as part of the “consume the Cargo crate, not the wheel” framing — by widening the library’s public surface, downstream wheels (kglite, others) can stay thin pyo3 wrappers instead of carrying business logic.

Tests

• from_manifest_resolves_full_stack — happy path: bundled + project + operator-declared paths compose through the one-shot call.

• from_manifest_surfaces_manifest_load_error — broken manifest YAML surfaces as SkillError::Manifest, not a downstream parsing error.

0.3.37 — 2026-05-14

Fixed — agent retrieval gap (the load-bearing one)

The auto-inject pass for auto_inject_hint: true skills previously appended a [See prompts/get <name> for full methodology.] pointer to the matched tool’s description. Agents in real MCP clients can’t reach prompts/get — Claude Code, Claude Desktop, Cursor, and Continue all expose only tools/* to the model; the prompts/* plane was designed for human-invoked slash commands. The pointer was a dangling reference; operator-authored methodology was unreachable by the agent.

This release replaces the pointer with full-body embedding under a ## Methodology header in the matched tool’s description. Bounded by the existing 4 KB soft / 16 KB hard size caps the framework enforces per skill. Operators who want the older pointer-shaped behaviour (or no inject at all) set auto_inject_hint: false per skill.

prompts/list and prompts/get continue to work — they’re still useful for MCP clients that do surface prompts to the agent, plus CLI introspection (mcp-server skills-show). The auto-inject path just becomes the primary delivery channel for the agentic clients in use today.

Found by an mcp-servers operator deploying kglite 0.9.31 + mcp-methods 0.3.36 against a live Claude Code session. Their three eval queries passed only because graph_overview happened to inline schema + methodology in one tool response; skills with non-parallel property prefixes, multi-hop temporal idioms, or out-of-schema content would have failed silently.

Fixed — silent file-drop on YAML parse error

SkillRegistry.from_manifest previously silently skipped any SKILL.md whose frontmatter failed to parse. The intent was “one broken skill in a domain pack shouldn’t take down the rest” — but the surface was too silent: operators hitting an unquoted colon in a description (First clause: second clause, which PyYAML reads as a mapping value separator) spent 25-minute debug sessions wondering why their override “took” but didn’t show up in prompts/list.

Two-channel fix:

1. tracing::warn! continues to fire per dropped file. Operators with structured tracing get the warning immediately.

2. New ResolvedRegistry.parse_warnings() Rust getter and SkillRegistry.parse_warnings Python getter — durable structured surface that downstream binaries can render in their boot summary. Returns Vec<ParseWarning> (Rust) or list[dict] (Python) with per-file path + error.

let registry = SkillRegistry::new()
    .auto_detect_project_layer(&yaml_path)
    .finalise()?;
for warning in registry.parse_warnings() {
    eprintln!("skill drop: {} — {}", warning.path.display(), warning.error);
}

reg = SkillRegistry.from_manifest("./my_mcp.yaml")
for w in reg.parse_warnings():
    print(f"skill drop: {w['path']} — {w['error']}")

Same pattern as the existing (no .env found) boot lines downstream binaries already render — operators internalised that channel.

Tests + docs

• load_skills_from_dir_surfaces_yaml_parse_failure_as_warning — reproduces the operator’s colon-in-description scenario; good skill still loads, broken file surfaces as a structured warning.

• resolved_registry_parse_warnings_propagated_from_project_layer — end-to-end through Registry::finalise.

• serve_prompts_auto_injects_full_body_into_matching_tool — replaces the pre-0.3.37 pointer-assertion test; now asserts ## Methodology header + body sentinel are present, and that prompts/get is not referenced (anti-regression).

• docs/guides/writing-effective-skills.md gains a “How skill bodies reach the agent” section explaining the retrieval-gap rationale and authoring implications.

Backwards compatibility

• A skill without auto_inject_hint (or with auto_inject_hint: true, the default) now produces a larger tool description than in 0.3.36. The size is bounded by the per-skill caps; operators who want the old behaviour set auto_inject_hint: false.

• parse_warnings is a new field on ResolvedRegistry — additive, doesn’t break any existing usage.

• The load_skills_from_dir function’s return type changed from Result<Vec<Skill>, _> to Result<(Vec<Skill>, Vec<ParseWarning>), _>. This is technically a breaking change for anyone calling that function directly, but kglite’s audit and our own grep confirmed no downstream consumers reach for it — they go through Registry::finalise instead.

0.3.36 — 2026-05-14

Added — applies_when: predicate gating on individual skills

Skills can now declare predicate conditions for activation. Skills with applies_when: predicates that don’t evaluate to true are silently omitted from prompts/list and prompts/get. Inspired by kglite’s three-deployment scenario (legal / o&g / code) where the same skill catalogue ships to every deployment but only some skills should fire per-graph.

---
name: read_code_source
description: Resolve qualified_name → source slice. TRIGGER when ...
applies_when:
  graph_has_node_type: [Function, Class]
  graph_has_property: { node_type: Function, prop_name: module }
  tool_registered: cypher_query
  extension_enabled: csv_http_server
---

Bounded predicate set — not a DSL. All populated predicates are ANDed. Predicate categories:

• Framework-internal — tool_registered, extension_enabled. Dispatched against ServerOptions.{tool_router, extensions} without consulting any evaluator.

• Domain — graph_has_node_type, graph_has_property. Dispatched via the new SkillPredicateEvaluator trait. Downstream binaries register one with Registry::with_predicate_evaluator(...) before finalise().

Evaluators that don’t recognise a clause return None; the framework records Unknown and treats it as inactive — safer than silently activating the wrong-domain skill.

Behaviour split: operator-facing vs agent-facing

• Agent-facing prompts/list / prompts/get — inactive skills are silently omitted. tracing::info! logs the failed clauses so the boot log carries full attribution.

• Operator-facing mcp-server skills-list — shows every resolved skill with an active/inactive column and indented per-clause outcomes for inactive ones. Mirrors the existing loud-collision pattern.

Mirrors the existing split for workspace activation: operator sees full provenance, agent sees only the resolved choice.

ServerOptions.extensions field

ServerOptions gains an extensions: serde_json::Map<String, Value> field, populated from the manifest’s extensions: block by from_manifest. Empty map when no extensions: block is present.

Downstream binaries that previously read Manifest.extensions directly can now read the same data off ServerOptions without re-loading the manifest. The framework uses this internally for the extension_enabled: predicate.

Python surface — Skill.applies_when

mcp_methods.Skill gains an applies_when getter returning a dict | None. Python operators can pre-filter their registries before calling register_skills_as_prompts:

for skill in registry.skills():
    if skill.applies_when and "graph_has_node_type" in skill.applies_when:
        # filter against our domain state, skip if predicate fails
        ...

The Python SkillPredicateEvaluator trait is not surfaced in this release — operators who need domain predicate dispatch from Python should pre-filter manually using applies_when introspection. Native Python evaluator support requires a Python-callable → Rust-trait bridge that’s deferred to a future release.

Backwards compatibility

A SKILL.md without applies_when: is always active — every existing skill keeps working unchanged. The tool_registered and extension_enabled framework-internal predicates work without any evaluator wired in, so single-domain consumers get most of the predicate engine for free.

0.3.35 — 2026-05-14

Added — skills-aware MCP via the prompts/ namespace

A new top-level manifest field, skills:, opts a deployment into shipping operator-authored methodology as MCP prompts. The three-layer composition is project → domain pack → bundled defaults, with later-layer (i.e. project) entries fully replacing same-named entries in the lower layers:

name: kglite-mcp-server
skills:
  - true                    # framework defaults (5 bundled skills)
  - ./my-skills/            # domain skill-pack (operator-declared dir)

Polymorphic shape: skills: false (default), skills: true (bundled only), skills: ./path/ (one domain pack), or a list mixing booleans and paths. The auto-detected project layer is <basename>.skills/ adjacent to the manifest YAML — if present, it wins over both domain-pack and bundled.

Bundled framework defaults ship five SKILL.md files (grep, read_source, list_source, github_issues, repo_management) that operators inherit when skills: true. Downstream binaries can add their own bundled layer via Registry::add_bundled_many(...) before finalising.

Wiring helpers for downstream binaries

Downstream binaries reach the wiring with roughly ten lines of glue:

let manifest = mcp_methods::server::load_manifest(&path)?;
let registry = mcp_methods::server::SkillRegistry::new()
    .merge_framework_defaults()
    .auto_detect_project_layer(&path)
    .layer_dirs(&manifest.skills, &path)?
    .finalise()?;
let mut server = mcp_methods::server::McpServer::new(opts);
mcp_methods::server::serve_prompts(&registry, &mut server);

serve_prompts(registry, server) populates the prompts/list / prompts/get surface and applies an auto-injection pass on tool descriptions: skills with auto_inject_hint: true whose name matches a registered tool get a “see prompts/get <name> for full methodology” pointer appended to that tool’s description, so agents who only read tools/list can still find the methodology.

Zero impact on existing deployments

A manifest with no skills: declaration is a verbatim-current deploy: no prompts/ capability advertised in get_info, no behavioural diff. The constraint is enforced at the type level via SkillsSource::Disabled (the default) and at the runtime level via the empty prompt_router — the rmcp default list_prompts / get_prompt impls return empty / not-found when no skills are registered.

Python bindings

mcp_methods.SkillRegistry and mcp_methods.Skill ship as thin pyo3 wrappers (newtype + delegate). SkillRegistry.from_manifest(path, include_bundled=True) builds the registry; register_skills_as_prompts(app, registry) in mcp_methods.fastmcp wires it into a FastMCP server in one call. The framework crate (mcp-methods) remains pyo3-free; the CI gate (cargo tree -p mcp-methods -e all | grep pyo3 returns empty) is unchanged.

Frontmatter schema

Each SKILL.md file ships YAML frontmatter for metadata:

---
name: cypher_query
description: One-line summary for `prompts/list`.
applies_to:
  mcp_methods: ">=0.3.35"
references_tools:
  - cypher_query
references_arguments:
  - cypher_query.format
auto_inject_hint: true     # default
applies_when: []           # phase-3 predicate hooks; parsed but inert
---

# Methodology body in markdown...

name and description are required; everything else is optional. The applies_when: predicate evaluator is deferred to a later release — predicates parse but don’t gate yet.

Size limits

The registry enforces three soft/hard caps to keep the prompt surface healthy: 4 KB lint-warns, 16 KB hard-fails a single skill, 64 KB caps the resolved-set total. The framework’s bundled skills round-trip through CI tests that pin the limits.

Bundled-skill rewrite + authoring template

The five bundled skills (grep, read_source, list_source, github_issues, repo_management) ship with rewritten descriptions and bodies aligned to the patterns Anthropic publishes for their own skills at github.com/anthropics/skills. Descriptions grew from ~15 words to 80-140 words with explicit TRIGGER / SKIP language (the recommended shape for combating Claude’s tendency to undertrigger). Bodies gained Quick Reference tables, Common Pitfalls sections with ❌/✅ markers, and (for github_issues) an ASCII decision tree mapping user phrasings to the three modes.

Operators authoring their own skills get a scaffold helper:

mcp-server skills-new ./my.skills/ my_method "TRIGGER when ..."

mcp_methods.write_skill_template("./my.skills/", name="my_method", description="TRIGGER when ...")

The template emits a parse-valid SKILL.md with the body skeleton (Overview → Quick Reference → Common Pitfalls → “When wrong”) and the optional extension fields commented out. Empty descriptions are refused — a blank description guarantees the skill will never trigger.

A new docs guide, Writing Effective Skills, distils the patterns from Anthropic’s published skills repo plus their best-practices doc.

0.3.34 — 2026-05-14

Added — tools[].bundled: rename: per-deployment tool aliasing

The bundled-override shape from 0.3.31 gains a third axis:

tools:
  - bundled: cypher_query
    rename: legal_cypher_query           # expose to agent under a different name
    description: "Cypher against the legal corpus knowledge graph."
  - bundled: graph_overview
    rename: legal_graph_overview
  - bundled: ping
    hidden: true

Use case: when an operator runs multiple downstream servers each backed by a different data source (e.g. three kglite-mcp-servers for open_source, legal, prospect), the bundled tool names collide across servers and MCP ToolSearch results rank them near-identically. The agent can’t disambiguate which cypher_query to use. Rename lets each deployment expose distinct names — open_source_cypher_query, legal_cypher_query, prospect_cypher_query — so search ranking and tool selection behave correctly.

The rename composes with the existing description: and hidden: axes; an override can use any combination.

Schema

Field	Type	Default	Notes
rename:	string	unset	Replaces the bundled tool’s agent-facing name. Must be a valid identifier (^[a-zA-Z_][a-zA-Z0-9_]*$). None means “keep the original bundled name.”

Permitted alongside bundled:, description:, hidden:. Forbidden on tool-creation (cypher: / python:) entries — the override-only constraint from 0.3.31 still applies.

Framework records, consumer enforces

The framework parses rename: and surfaces it via BundledOverride.rename and Manifest::to_json(). It does not validate that the renamed name collides with another tool (bundled, cypher, or python) in the manifest — the framework doesn’t know the downstream binary’s full bundled-tool catalogue, so collision detection has to live in the consumer.

The kglite consumer landing in 0.9.30 does this check at boot: “rename doesn’t shadow any other registered tool” → exit cleanly with a clear error if it does. Same pattern as advisory trust gates: framework declares, consumer enforces.

JSON shape addition

Manifest::to_json() emits the new field on bundled entries:

{
  "kind": "bundled",
  "name": "cypher_query",
  "rename": "legal_cypher_query",   // null when not declared
  "description": "...",
  "hidden": false
}

Non-breaking under the existing JSON-shape stability guarantee — consumers that ignore unknown keys keep working; consumers that want rename support match on the rename key.

Rust API change (heads up)

BundledOverride struct gains a rename: Option<String> field. Consumers destructuring this struct will get a compile error and need to handle the new field:

// Before 0.3.34
let BundledOverride { name, description, hidden } = &override_spec;
// After 0.3.34 — compile error: field `rename` missing
let BundledOverride { name, description, hidden, rename } = &override_spec;

Non-exhaustive struct attribute isn’t applied — additions remain visible at consumer-build time, which is the right failure mode for adding new fields to a public struct.

Tests

Six new tests in manifest.rs::tests under the bundled_* family:

• bundled_rename_parses_when_valid_identifier — happy path

• bundled_rename_alongside_description_parses — composes with description:

• bundled_rename_defaults_to_none — omitting rename: produces None

• rejects_bundled_rename_with_invalid_identifier — 123-bad rejected

• rejects_bundled_rename_with_non_string_value — 42 rejected

• bundled_rename_serialises_to_json — JSON shape addition verified

123 mcp-methods unit tests pass (was 117 at 0.3.33; +6 net). 7 deployed_manifests + 7 mcp-server tests unchanged.

Origin

Reported by the mcp-servers operator’s post-0.9.29 ToolSearch audit: multiple kglite servers with identical tool surfaces caused ranking ambiguity. kglite implemented the framework half and pushed it to this tree; reviewed, no design changes needed.

0.3.33 — 2026-05-14

Changed — workspace.applies_to now accepts glob patterns + lists

The opt-in declaration introduced in 0.3.32 was a single literal path string. 0.3.33 widens it to three shapes:

workspace:
  # 1. Literal pattern (existing in 0.3.32) — match this exact name
  applies_to: ./repos

  # 2. Glob pattern (NEW) — match a subset by naming convention
  applies_to: ./prod-*      # any child whose name starts with "prod-"
  applies_to: ./*           # any direct child (wildcard)
  applies_to: ./test-?      # one-char suffix variant

  # 3. List of patterns (NEW) — match if any pattern matches
  applies_to: [./repos, ./clones]
  applies_to: [./prod-*, ./test-*]   # multiple naming conventions

Glob syntax follows globset (the ripgrep/cargo crate): * (any chars), ? (one char), [abc] (character class), ** (any depth — irrelevant here since the parent-walk is single-level).

The opt-in semantics are unchanged: when the parent-walk fallback finds a manifest, the framework compares the actual workspace_dir’s basename against the declared pattern(s). Match → use the manifest. No match or no declaration → operator must pass --mcp-config explicitly. The accidental-discovery footgun stays closed; this release just widens what an author can opt into.

Use case

Operators with a repos/ sandbox containing many projects no longer need to enumerate each child:

repos/
├── workspace_mcp.yaml      # applies_to: ./*
├── project-alpha/          # --workspace repos/project-alpha/  ✓
├── project-beta/           # --workspace repos/project-beta/   ✓
└── client-acme/            # --workspace repos/client-acme/    ✓

Or filter by naming convention:

deployments/
├── workspace_mcp.yaml      # applies_to: ./prod-*
├── prod-api/               # ✓
├── prod-web/               # ✓
├── stage-api/              # ✗  (parent-walk discovery refuses)
└── test-runner/            # ✗

Parse-time validation

Patterns are validated at boot via globset::Glob::new:

• Empty patterns rejected (applies_to: "")

• Multi-segment paths rejected (applies_to: ./a/b/c — parent-walk is single-level, so deeper paths could never match)

• Parent-relative rejected (applies_to: ..)

• Absolute paths rejected (applies_to: /abs/foo)

• Invalid glob syntax rejected (e.g. unterminated [)

Operators get a clear error at boot rather than silent non-matching.

Internal shape change

WorkspaceConfig::applies_to changed from Option<String> to Option<AppliesTo> where:

pub enum AppliesTo {
    Pattern(String),         // single pattern
    Patterns(Vec<String>),   // multiple patterns
}

Leading ./ is stripped at parse time (storage is normalised). This is a Rust-API surface change since 0.3.32; consumers that read manifest.workspace.applies_to need to handle the enum.

JSON shape change

Manifest::to_json() now emits workspace.applies_to polymorphically:

• Pattern("repos") → "repos" (string)

• Patterns(["repos", "clones"]) → ["repos", "clones"] (array)

• None → null

Mirrors the YAML shape. Consumers should accept both types.

New dependency

Direct dependency on globset = "0.4" added to mcp-methods. The crate was already a transitive dep via ignore; making it direct just lets the manifest parser validate glob patterns at boot.

Tests

Six new tests in manifest.rs::tests:

• find_workspace_applies_to_wildcard_matches_any_child — * matches three different child names

• find_workspace_applies_to_glob_matches_prefix — ./prod-* matches prod-api/prod-web but not test-*

• find_workspace_applies_to_list_matches_any_entry — [./repos, ./clones] matches either, rejects others

• applies_to_rejects_deep_path_at_parse_time — ./a/b/c errors at boot

• applies_to_rejects_invalid_glob_at_parse_time — ./[unterminated errors at boot

• applies_to_rejects_parent_relative — .. and ../up both error

117 mcp-methods unit tests pass (was 111 at 0.3.32; +6 net). 7 deployed_manifests + 7 mcp-server tests unchanged.

Origin

Operator scenario raised by Kristian: a repos/ directory holding many child repos, with one manifest covering them all. Single-path match didn’t cover this; glob + list shapes do.

0.3.32 — 2026-05-14

Changed — find_workspace_manifest parent-walk fallback (opt-in)

find_workspace_manifest(workspace_dir) now also looks one level up for workspace_mcp.yaml, but only when the parent manifest declares it applies to the given workspace dir via a new field:

# open_source/workspace_mcp.yaml
workspace:
  kind: github
  applies_to: ./repos    # opt-in: parent-walk auto-detection allowed
                         # for `--workspace open_source/repos/`

When the operator passes --workspace open_source/repos/:

1. Primary location (open_source/repos/workspace_mcp.yaml) is checked first; if present, it wins unconditionally.

2. If absent, the parent (open_source/workspace_mcp.yaml) is considered — but only if it declares workspace.applies_to: ./repos AND that path canonicalises to the actual workspace_dir.

Without the declaration (or with a mismatched path), the framework refuses to auto-detect — operator must pass --mcp-config explicitly. The opt-in eliminates the accidental-discovery footgun where a project-root manifest would silently attach to any sibling dir an operator happened to pass to --workspace.

Why opt-in

The original design considered an unconditional parent-walk fallback. That would have introduced a regression: an operator with ~/proj/workspace_mcp.yaml (for their real workspace) accidentally running mcp-server --workspace ~/proj/some_other_dir/ would silently inherit the wrong manifest. The opt-in eliminates this entirely — the manifest author declares which child the manifest covers, and the framework only matches that declaration.

The natural layout this enables:

open_source/
├── workspace_mcp.yaml     # declares workspace.applies_to: ./repos
└── repos/                 # --workspace points here; auto-detect works

Operators in this layout no longer pass --mcp-config for every workspace launch.

New schema field

workspace.applies_to: <relative path> — optional string, must be non-empty when set. Resolved against the manifest’s parent directory. Unset = no parent-walk discovery for this manifest (the safe default for existing manifests).

Manifest::to_json() emits the new field under workspace.applies_to (string or null). Non-breaking JSON shape addition under the existing stability guarantee.

Logging

When the parent-walk fallback is considered, the framework emits a tracing log at INFO level explaining the discovery outcome:

• "manifest discovered via parent-walk fallback (workspace.applies_to matched)" — on success

• "parent-walk manifest does not declare workspace.applies_to; ignoring" — declaration absent

• "parent-walk manifest's workspace.applies_to does not match this workspace_dir; ignoring" — mismatch

Operators with RUST_LOG=info (or any tracing subscriber wired up by their binary, which mcp-server’s init_tracing does by default) see exactly why discovery did or did not succeed.

Tests

Six tests under find_workspace_*:

• find_workspace_works — primary location (existing).

• find_workspace_walks_one_level_up_with_applies_to — opt-in match returns the parent manifest.

• find_workspace_ignores_parent_without_applies_to — parent manifest without declaration is NOT auto-detected.

• find_workspace_ignores_parent_with_mismatched_applies_to — declaration that doesn’t match is rejected.

• find_workspace_returns_none_when_missing_everywhere — no manifest in child or parent → None.

• find_workspace_primary_wins_over_parent_fallback — primary always preempts even when both could match.

111 unit tests pass (was 108 at 0.3.31 head; +3 net after refactor — two new opt-in tests, the existing walks-up test renamed to make the opt-in requirement explicit).

Origin

kglite operator audit during the 0.6.x → 0.9.x migration: workspace manifests sitting next to (not inside) the workspace dir required --mcp-config for every launch. They proposed and implemented the parent-walk in their local tree; we picked the opt-in shape over their unconditional version to eliminate the accidental-discovery risk.

0.3.31 — 2026-05-13

Added — tools[].bundled: override shape

Manifest tools: arrays now accept a third entry kind alongside cypher: and python:: bundled: entries customise the agent-facing surface of a bundled tool the downstream binary provides natively (e.g. cypher_query, repo_management, graph_overview).

tools:
  - bundled: repo_management        # name in the value, no `name:` line
    description: |                  # override the agent-visible description
      FIRST STEP for this server. Call repo_management('org/repo')
      to clone + build a repo before any other tool.

  - bundled: ping                   # hide a tool from tools/list AND
    hidden: true                    # reject calls to it

  - name: similar_sessions          # existing cypher-tool shape unchanged
    cypher: |
      MATCH ...

Field semantics:

Field	Type	Default	Notes
bundled:	string	(required)	The bundled tool’s name. Must match ^[a-zA-Z_][a-zA-Z0-9_]*$. The framework does NOT validate against an actual catalogue (it doesn’t know what bundled tools the downstream binary provides); the consumer is responsible for “unknown tool name” errors at boot.
description:	string	None	Replaces the bundled tool’s default agent-facing description. None means “keep the default.”
hidden:	bool	false	When true, the downstream consumer should omit the tool from tools/list AND reject calls to it.

Mutually exclusive with cypher: / python: / name: / parameters: / function:. The parser surfaces clear errors at boot for combinations that don’t fit.

Motivation

The pre-0.3.31 customisation surface for bundled tools was the manifest’s global instructions: block — useful for first-message agent orientation, but a single blob detached from individual tools. Operators wanting to teach agents that repo_management is the FIRST STEP, or hide ping from a production server, had to stuff that into the global instructions and hope the agent correlates it. Bundled overrides attach those concerns to the tools directly: descriptions ride the tools/list response next to the schemas, and hidden:true is the surgical opt-out for “this tool is in the bundled catalogue but my agent shouldn’t see it.”

The downstream kglite-mcp-server is the first consumer; it ships bundled-override support in its next release after this lands. The framework half of the work is small (~150 LoC parser + struct + to_json variant + 11 tests) and entirely additive — pre-existing tools[].cypher and tools[].python entries parse unchanged.

JSON shape addition

Manifest::to_json() emits bundled override entries as:

{
  "kind": "bundled",
  "name": "repo_management",
  "description": "FIRST STEP for this server...",
  "hidden": false
}

Non-breaking field addition to the existing tools[] array shape. Consumers that ignore unknown kind values stay safe; consumers that want bundled-override support match on kind == "bundled".

Tests

11 new parser tests in crates/mcp-methods/src/server/manifest.rs::tests:

• bundled_override_with_description_parses

• bundled_override_with_hidden_parses

• bundled_override_alongside_cypher_tools_parses

• rejects_bundled_with_cypher_kind

• rejects_bundled_with_name_field

• rejects_bundled_with_parameters_field

• rejects_bundled_with_non_bool_hidden

• rejects_hidden_on_cypher_tool

• rejects_duplicate_bundled_overrides

• rejects_bundled_with_invalid_identifier

• bundled_override_to_json_shape

Plus the existing 93 mcp-methods tests stay green (additive change; no behaviour shift on the cypher / python paths).

Fixed — repo_management cross-binary surface drift

The generic mcp-server CLI used to always register repo_management in tools/list, regardless of whether a workspace was bound. Without a workspace, calls to the tool returned "repo_management requires --workspace mode." — but the tool was still visible to the agent.

Downstream binaries (e.g. kglite-mcp-server) gate the same tool out of tools/list entirely when no workspace is bound. The inconsistency surfaced when operators ran the same YAML against mcp-server (saw the tool) and kglite-mcp-server (didn’t see it).

McpServer::new now calls tool_router.remove_route("repo_management") when options.workspace.is_none(). Tool surface matches downstream gating; agents only see the tool when it can do something useful.

Two new tests anchor the behaviour:

• repo_management_gated_to_workspace_mode — bare framework, no workspace, tool is absent from list_all().

• repo_management_present_when_workspace_bound — with a workspace, tool is present.

Reported by kglite while comparing the two binaries against the same YAML post-0.9.25 deployment.

0.3.30 — 2026-05-12

Distribution shape — bundled binary in the pip wheel

pip install mcp-methods now puts the mcp-server CLI on PATH again, restoring the pattern we shipped in 0.3.25. The wheel bundles the native Rust binary at mcp_methods/_bin/mcp-server; the Python entry point mcp_methods._cli:main execs it on invocation.

This is the kglite-style “pip install gives you everything” UX, adapted for our case: because our mcp-server binary has zero libpython link (kept from the 0.3.26 pure-Rust separation), we stay at 3 abi3 wheels per OS — no per-Python-version matrix.

Why the revert

The 0.3.26 polars-shape split removed the bundled binary on architectural grounds. Re-introducing it: pip is the operator-facing distribution and the CLI is the operator-facing artefact. A separate crates.io entry for mcp-server (the 0.3.29 plan) would have added a distribution path nobody asked for. Single distribution path is clearer.

crates/mcp-server/ stays in the workspace as the binary’s source home — used by the wheel build to compile + bundle, and available for downstream Rust users via cargo install --git. Not published to crates.io.

crates.io — library publication

mcp-methods 0.3.30 is the first version published to crates.io. The library is pure Rust, zero pyo3 in the dep tree (the polars shape from 0.3.26 is preserved). docs.rs auto-builds the rustdoc. Downstream consumers can now write:

mcp-methods = "0.3"

…instead of pinning to a git rev. kglite’s existing git-rev pin keeps working unchanged.

Files touched

• pyproject.toml — restored [project.scripts] + [tool.maturin] include blocks.

• python/mcp_methods/_cli.py — restored.

• Makefile — restored bundle-bin / dev-with-bin targets.

• .github/workflows/build_wheels.yml — restored the cargo-build-binary + copy-into-wheel step (per-OS).

• .gitignore — re-ignore python/mcp_methods/_bin/.

• crates/mcp-methods/Cargo.toml — publish metadata (repository, keywords, categories, docs.rs config).

• crates/mcp-server/Cargo.toml — version 0.3.29 → 0.3.30 (still workspace-local; not published).

• README.md — drop the cargo install mcp-server section; fold the CLI into the Python-install path.

No regression for downstream Rust consumers

The library crate source is unchanged. kglite’s rev = "71f7ba6..." pin resolves identically. The new 0.3.30 publish to crates.io is opt-in — downstream consumers who want to switch from git-rev to version = "0.3" can, but nothing forces them.

0.3.29 — 2026-05-12

Added

• trust.allow_query_preprocessor — third advisory trust gate alongside allow_python_tools and allow_embedder. The framework parses the bool and surfaces it through TrustConfig and Manifest::to_json(); downstream consumers enforce. Mirrors the existing allow_embedder pattern: the framework records the operator’s declared trust, the consumer (e.g. kglite-mcp-server) refuses to boot the corresponding extension hook when the flag is false. Driven by the mcp-servers-operator’s 0.9.25 Cypher preprocessor spec.

JSON shape

• Manifest::to_json() now emits trust.allow_query_preprocessor. Non-breaking field addition; consumers that ignore unknown keys are unaffected. The to_json_shape_is_stable snapshot test has been updated to expect the new key.

Tests

• allow_query_preprocessor_trust_parses — positive case.

• allow_query_preprocessor_rejects_non_bool — type validation.

0.3.28 — 2026-05-12

Fixed

• Workspace::set_root_dir no longer clobbers the just-set active_repo_path back to the configured workspace_dir. The local-mode branch of clone_or_update now reads the current active_repo_path from state (falling back to workspace_dir only when state is unset), so the activate-after-set_root_dir sequence preserves the new root, and the post-activate hook fires against the bound target rather than the original configured root.

  Reported by kglite while wrapping Workspace in pyo3 for 0.9.24. Bug had no effect on github-mode workspaces; only local-mode set_root_dir callers who read active_repo_path() after the swap (or whose post-activate hook needed to rebuild against the new root) were affected.

Added (tests)

• set_root_dir_updates_active_path — anchors the invariant.

• set_root_dir_post_activate_fires_against_new_root — confirms the hook fires against the bound target.

0.3.27 — 2026-05-12

Added

• Manifest::to_json() -> serde_json::Value for FFI / RPC introspection. Returns a JSON-friendly view of the validated manifest with stable shape across patch releases. Intended for pyo3 wrappers, JSON-RPC bridges, and any consumer that needs programmatic access to the loaded manifest without per-field getters. Schema knowledge lives end-to-end on the framework side; downstream wrappers shrink to roughly one passthrough method plus a generic serde_json::Value -> PyObject (or equivalent) converter.

Notes

• No breaking changes. No new dependencies (serde_json was already in the dep tree).

• The JSON shape is pinned by the to_json_shape_is_stable test in crates/mcp-methods/src/server/manifest.rs — read it as the canonical contract. Future renames or removals in this shape are breaking changes; additions are non-breaking.

• No #[derive(Serialize)] on any manifest struct: keeps the hand-rolled parsing symmetry on input and output, and avoids coupling JSON shape to Rust field names.

0.3.26

The polars / pydantic-core distribution shape. mcp-methods is now a pure-Rust library with zero PyO3 in source or deps; the Python wheel is built from a separate mcp-methods-py binding crate. cargo add mcp-methods from Rust sees no traces of Python anywhere.

Workspace restructure

Three-crate workspace (one was four-crate-ish in 0.3.25 with bundled- binary machinery; that’s gone too):

• crates/mcp-methods — pure-Rust library (rlib only). Contains every primitive (cache, compact, files, git_refs, github, grep, html, json_grep, list_dir) plus the server framework module behind the default-on server feature. No pyo3, no #[pyfunction], no Py<…>, no PyResult anywhere in the source. CI verifies via cargo tree -p mcp-methods | grep pyo3 as a fail-on-leak gate.

• crates/mcp-methods-py — PyO3 bindings crate (cdylib only). Depends on mcp-methods and provides #[pyfunction] / #[pyclass] wrappers around the library functions. PyElementCache is a newtype wrapper over mcp_methods::cache::ElementCache. The wheel is built from this crate via pyproject.toml’s manifest-path setting.

• crates/mcp-server — standalone CLI binary. Depends on mcp-methods with features = ["server"]. Published to crates.io alongside the library; install via cargo install mcp-server.

Distribution

Audience	Command	Result
Rust library users	cargo add mcp-methods	Pure-Rust crate. No pyo3 in dep tree.
Python users	pip install mcp-methods	One abi3 wheel per OS (3 total) — works on Python 3.10 through 3.13 without reinstall. Down from 12 per-Python-version wheels in 0.3.25.
CLI users	cargo install mcp-server	Binary on PATH. No libpython link.

The bundled-binary mechanism from 0.3.25 is gone: no more mcp_methods/_bin/, no _cli.py Python launcher, no [project.scripts] entry, no maturin include for the binary, no make bundle-bin. pip install mcp-methods ships only the cdylib and Python wrapper; the binary lives in its own crate.

Python embedder: / tools[].python: removed

The legacy framework hooks for loading Python embedder classes and Python tool callables were removed. They required PyO3 in the framework’s source — incompatible with the pure-Rust contract. No deployed manifest uses tools[].python:, and the lone embedder consumer (kglite’s sodir / norwegian_law / petrel servers) migrated to fastembed-rs in 0.9.18. Downstream binaries that need Python extension hooks add a pyo3 wrapper layer in their own cdylib.

API shape changes

Callback-bound functions kept their Python-side surface (the wheel’s read_file(transform=…), list_dir(annotate=…), ripgrep_files(transform=…) still take callables). On the Rust side, the callback is now a generic &dyn Fn(...) parameter on a ReadFileOpts / ListDirOpts / RipgrepFilesOpts struct. Pure-Rust callers default-construct the opts and skip the callback; the binding crate bridges Py<PyAny> → Rust closure that re-enters Python via Python::attach.

compact_discussion returns Result<(String, Option<String>), String> in Rust; the binding crate’s wrapper maps to PyValueError. ripgrep_lines and ripgrep_json_fields return typed Vec<RipgrepLinesGroup> / Vec<JsonGrepMatch>; the wrapper converts to Python lists of dicts.

Migration

For Python users: zero changes. from mcp_methods import … imports identical. Wheel layout (mcp_methods/_mcp_methods.so) preserved.

For Rust library consumers (kglite, etc.): Cargo.toml stays the same — mcp-methods = { …, features = ["server"] } still works because we kept the server feature default-on. Source paths are unchanged: mcp_methods::server::McpServer, mcp_methods::cache::ElementCache, mcp_methods::github::fetch_issue_internal, etc. — all in the same locations. Two things to know about:

• mcp_methods::server::embedder and mcp_methods::server::python modules are gone. kglite stopped using them in 0.9.18; if a future consumer needed them, they re-implement in their own pyo3 crate.

• mcp_methods::server::apply_python_extensions and PythonExtensions are gone for the same reason.

For CLI users: the binary distribution changed. Old: pip install mcp-methods put it on PATH. New: cargo install mcp-server. Reflects the binary’s actual nature (a Rust CLI tool, not a Python package).

Tests

87 cargo unit tests + 7 mcp-methods integration tests + 7 mcp-server binary tests + 176 python tests = 277 total. cargo tree -p mcp-methods | grep pyo3 is a CI gate; if it ever returns non-zero, the build fails.

0.3.25

Structural consolidation + the long-tail of the PyO3 decoupling work. This release closes both distribution goals: pip install mcp-methods puts mcp-server on PATH, and downstream Rust binaries (kglite-mcp-server, etc.) can build with no transitive libpython linkage via default-features = false.

Workspace consolidation

• crates/mcp-server is gone. Its modules moved into the root mcp-methods crate under a new server feature. Every public type and function name is preserved — paths shift by one segment:

  • mcp_server::McpServer → mcp_methods::server::McpServer

  • mcp_server::manifest::ToolSpec → mcp_methods::server::manifest::ToolSpec

  • mcp_server::build_tool_attr → mcp_methods::server::build_tool_attr

  • etc.

• Lib name renamed _mcp_methods → mcp_methods. The leading- underscore convention is Python-internal; in Rust it forced consumers to write use _mcp_methods::*. Now they write use mcp_methods::*. Python’s from mcp_methods._mcp_methods import … still works — maturin’s module-name override places the cdylib at the same wheel path as before.

• crate::cache::ElementCache, crate::github::*, crate::git_refs::*, crate::compact::*, crate::html::* stay at the crate root — intra-crate references shift from _mcp_methods::* to crate::*.

pip install mcp-methods ships mcp-server on PATH

• Wheel now bundles the native Rust binary under mcp_methods/_bin/mcp-server and registers a Python console-script entry point (mcp-server = "mcp_methods._cli:main") that execs it.

• make dev-with-bin builds + bundles the binary locally; the wheel- build CI workflow runs the same sequence before maturin packages.

• Per-platform wheel size grows ~10 MB (the native binary).

Cargo features

The crate’s feature surface is now coherent across both build modes:

• default = ["python", "server"] — standard cargo install or wheel build path includes everything.

• python — opt-out drops PyO3 (no _mcp_methods cdylib, no callback-bound helpers like read_file/ripgrep/list_dir/ json_grep, no manifest-declared python: tools or embedder: blocks).

• server — opt-out drops rmcp + tokio + clap + the framework modules + the mcp-server binary.

• python-extension — implies python, adds pyo3/extension-module for the wheel cdylib.

A --no-default-features build is the pure-Rust primitives subset. A --no-default-features --features server build is the framework-only path with no libpython linkage — verified with otool -L target/debug/mcp-server showing no libpython3.x.dylib.

Downstream migration (kglite + similar)

# Before — two separate deps:
mcp-methods = { git = "...", rev = "0.3.24", default-features = false }
mcp-server  = { git = "...", rev = "0.3.24", default-features = false }

# After — one dep with the `server` feature:
mcp-methods = { git = "...", rev = "0.3.25", default-features = false, features = ["server"] }

Source rename pattern: mcp_server::X → mcp_methods::server::X; _mcp_methods::X → mcp_methods::X.

CI

• Workspace-root rows added: cargo build/test, cargo build/test --no-default-features, cargo build/test --no-default-features --features server.

• Wheel-build workflow updated to build + copy the bundled binary before maturin runs.

Tests

• 90 cargo unit tests (was 17 + 73 split across two crates) + 7 manifest regression + 7 binary CLI tests + 19 smoke + 157 python = 280 tests pass.

• All 5 deployed YAML manifests parse unchanged.

0.3.24

Responds to three kglite asks (inbox/read/2026-05-11-*). Three phases land together; consumer-visible APIs remain backward-compatible.

mcp-server framework

• extensions: top-level manifest passthrough. New top-level YAML key that the framework accepts but does not validate. Stored on Manifest as extensions: serde_json::Map<String, serde_json::Value>. Downstream binaries read whatever keys they need from it. Strict-unknown-key validation stays in force for the framework’s own surfaces (builtins:, workspace:, …) — only the extensions: block is intentionally unvalidated. Closes kglite’s csv-http extension ask; matches the domain-agnostic boundary set in 0.3.23.

• PyO3 is now an optional Cargo feature on crates/mcp-server. New python feature in crates/mcp-server/Cargo.toml, default-on. Standalone cargo install mcp-server is unchanged. Downstream binaries can disable with default-features = false to remove the direct PyO3 dep from this crate. Note: the top-level mcp-methods crate (the Python wheel) still depends on PyO3 unconditionally — that is by design. The feature flag on mcp-server removes the direct link from this crate only; for a fully PyO3-free downstream binary the consumer also needs to gate the mcp-methods dep itself. CI now runs both cargo build -p mcp-server --no-default-features and cargo test -p mcp-server --no-default-features to catch leaks.

• Cfg-gated modules: python.rs and embedder.rs are now #[cfg(feature = "python")]. runtime::PythonExtensions and runtime::apply_python_extensions are similarly gated. mcp-server binary’s main() emits a warn-level log if a manifest declares python: tools or embedder: in a binary built without the python feature, so operators aren’t silently ignored.

Tests + infrastructure

• Framework smoke-test suite. New tests/test_mcp_server_smoke.py drives the mcp-server binary over JSON-RPC stdio and exercises every tool category: source navigation, GitHub access (with and without token), .env walk-up + explicit env_file:, local- workspace mode, bare boot. 19 tests, ~3 seconds, auto-skips when the binary isn’t built. Adapted from kglite’s smoke suite shape; kglite-specific tests (graph / Cypher / read_code_source) stay in their repo.

0.3.23

Patch release in response to kglite’s 0.3.22 smoke-test findings (inbox/read/2026-05-10-from-kglite-smoke-test-findings.md). The framework stays domain-agnostic — Cypher tool registration is a graph-engine concern, so it stays on the kglite side. What we expose here is the primitive that lets downstream binaries build that registration cleanly.

mcp-server framework

• mcp_server::build_tool_attr now public. Closes the primitives half of Gap A: downstream binaries can now build the rmcp Tool attr from (name, description, json_schema) in the same shape the framework uses internally and pair it with ToolRoute::new_dyn to register their own dynamic tools — Cypher runners, custom DSL handlers, anything else. No API divergence between the framework’s own registrations and downstream ones.

mcp-methods (Rust core)

• auth_token filters empty strings. Closes Gap C: an env var set to "" (e.g. for clearing the token without unbinding) was reported as “token present” by has_git_token(), causing the github tools to register and then 401 on the first call. Now an empty string is treated identically to a missing var. Test added.

0.3.22

Closing the kglite wishlist gaps (inbox/read/2026-05-10) so the 5 deployed YAML manifests + ~3,000 LoC of custom Python MCP servers can retire onto this framework.

mcp-server framework

• .env auto-loading at startup. Walks upward from the workspace / source-root / watch / cwd looking for .env; loads KEY=VALUE lines into the process env (skip blanks/#, strip outer quotes, do not overwrite existing). Operators who want a non-implicit pick declare env_file: ../.env at the YAML top level.

• github_issues element drill-down. New element_id / lines / grep / context / refresh arguments on the MCP tool. FETCH responses cache collapsed cb_N / patch_N / comment_N / overflow elements server-side (via _mcp_methods::cache::ElementCache); pass element_id="cb_1" (with the same number=N) to retrieve a single element without re-fetching, optionally narrowed by lines="40-60" or grep="pat".

• Honest tool listing. github_issues and github_api are now registered dynamically at boot only when GITHUB_TOKEN is set; they no longer appear in tool-listing responses when the agent couldn’t use them. Boot-time decision — restart to pick up a token that appears later. The framework binary logs an info line announcing the skip.

• Workspace::last_built_sha(name). New public reader exposing the HEAD SHA persisted after the last successful post-activate hook for a repo. Backed by an additive last_built_sha field on the per-repo inventory.json entry (#[serde(default)] keeps older inventories loading cleanly). Foundation for the auto-rebuild-gating work landing in Phase C.

• Embedder lifecycle (mcp_server::embedder). New module exposing EmbedderHandle (load/unload/embed/touch + idle tracking) and spawn_idle_watch for the eviction tokio task. PythonExtensions now yields Option<Arc<EmbedderHandle>> plus embedder_cooldown and embedder_watcher. The framework owns the cooldown timer; the value is extracted from embedder.kwargs.cooldown in the manifest. Embedder classes must expose embed + dimension; load / unload are optional but called automatically when present.

• Manifest schema — new env_file: top-level key (added to ALLOWED_TOP_KEYS; strict-unknown-key validation preserved).

• Auto-rebuild gating on repo_management(update=True). Captures the new HEAD SHA on each clone/fetch; when the gate sees action == "current" AND prev_built_sha == new_head AND the user did not pass force_rebuild, the post-activate hook is skipped and the response carries a [build skipped: ...] marker. New force_rebuild: bool argument on the repo_management MCP tool bypasses the gate (useful after the builder itself has been upgraded).

• workspace.kind: local mode — new top-level manifest block workspace: { kind, root, watch }. kind: local binds a fixed directory as the source root and reuses the same auto-rebuild gating (with a cheap recursive-mtime fingerprint instead of git HEAD SHA). When the manifest declares kind: local, that wins over the CLI --workspace flag’s interpretation — manifest is the source of truth, same rule as source_root:. watch: true wires the framework’s debounced file watcher to the root for hot-reload rebuilds. Local mode rejects name= / delete=true in repo_management with a friendly error. New set_root_dir(path) MCP tool (registered automatically when in local mode) swaps the active root at runtime — drop-in for the legacy code_review server workflow. inventory.json is stored under <root>/.mcp-workspace/ in local mode to keep the user’s tree clean.

• McpServer::builtins() public getter. Surfaces the manifest’s builtins: block (save_graph, temp_cleanup) verbatim so downstream consumers (e.g. kglite’s graph_overview tool deciding whether to wipe temp/) can read the operator’s intent without re-parsing YAML. The framework does not act on these — it doesn’t know what an “overview” call means.

mcp_methods.fastmcp (Python)

New composable helpers for FastMCP authors so each one can drop the boilerplate that the YAML+CLI binary handles. Each helper takes the FastMCP app and the dependency it needs (graph, source roots, …) and registers the same tools the bundled binary ships, one-to-one.

• register_overview(app, graph, overview_prefix=None) — graph_overview.

• register_cypher_query(app, graph, csv_dir="temp/") — cypher_query with format="csv" writing uuid-named files for streaming/exports.

• register_source_tools(app, source_roots=[...]) — read_source, grep, list_source with the same path-sandbox semantics as the Rust framework (os.path.realpath rejects traversal). Wraps the existing PyO3 surface; ~10-line wrappers, no logic duplication.

• register_save_graph(app, graph) — save_graph(path).

• serve_csv_via_http(directory, port=0, bind="127.0.0.1") — CORS- enabled HTTP server for serving CSV exports to browser-side agent contexts. Returns (server, base_url); runs in a daemon thread.

A runnable end-to-end stub lives at examples/fastmcp_demo.py.

Documentation + regression suite

• README “Deployment” section. Documents the cargo install --path crates/mcp-server recipe, the symlink path for deployments that pinned a binary elsewhere, and a table of the operating modes (bare / source-root / workspace[github] / workspace[local] / watch) with how to set each via CLI flag or manifest.

• Regression test for deployed manifests. New integration test (crates/mcp-server/tests/deployed_manifests.rs) asserts the schema shapes used by the 5 production manifests at /Volumes/EksternalHome/Koding/MCP servers/ continue to load cleanly. If any starts failing after a schema change, a production manifest has been broken — fix the schema or migrate the deployment.

0.3.21

• McpServer::register_typed_tool<T, F>(name, description, handler) — typed dynamic-tool registration helper. Compresses the boilerplate of building a Tool attr from a JSON Schema (via schemars), serde- deserialising per-call arguments, and wrapping the handler in a ToolRoute::new_dyn closure. Domain binaries (kglite-mcp-server) use this to register their tools in ~5 lines instead of ~35. The handler is Fn(T) -> String; state lives in the closure environment.

0.3.20

Added — mcp-server crate (Rust-native MCP server framework + binary)

A new sibling crate at crates/mcp-server/ providing a Rust-native MCP server built on the official rmcp SDK (v1.6) with a stdio transport. Designed to replace the Python kglite.mcp_server over the next few phases. The new binary is mcp-server.

CLI refit — drop --graph (graph concept lives in downstream binaries like kglite-mcp-server, not in mcp-methods). Replace with --source-root DIR for direct binding of the source tools to a fixed directory. Modes are now: bare / --source-root / --workspace / --watch. Help text rewritten to clarify the framework’s domain- agnostic role; downstream binaries (kglite, etc.) layer their domain tools on top by re-using McpServer::new with custom registrations. Also dropped --embedder (the manifest’s embedder: block remains the source of truth).

Library extraction (post-phase-6). The crate now exposes a [lib] target alongside the [[bin]], with the framework boilerplate (apply_python_extensions, resolve_source_roots, init_tracing, maybe_watch) lifted into a new mcp_server::runtime module. This lets downstream binaries (kglite-mcp-server, etc.) reuse the entire boot sequence without copy-pasting hundreds of LoC of glue.

mcp_server::python::json_to_py is now pub so dynamic-tool implementations can reuse it for forwarding JSON kwargs to Python callables (e.g. graph.describe(**kwargs)).

Phase 6 — Workspace mode (--workspace DIR). Multi-repo clone-and-track flow with idle-sweep inventory.

• repo_management MCP tool: pass name='org/repo' to clone (if missing) and activate; delete=true to remove; update=true to fast-forward the active repo; no args to list with access counts.

• Active repo state lives in Workspace::Arc<RwLock<…>>; source tools pick up the swap on the very next call (with_workspace wires dynamic source-roots and default-repo providers).

• Inventory persists to <workspace>/inventory.json with cloned_at / last_accessed / access_count / stale per repo; reconciles with on-disk state at boot (un-tracked clones get inventory entries; vanished repos marked stale).

• Auto-sweeps idle repos older than --stale-after-days (default 7); active repo is exempt; stale entries preserve their access history even after deletion.

• Git operations shell out to git (clone –depth 1, fetch + reset –hard FETCH_HEAD); no libgit2 dep.

• PostActivateHook callback type lets downstream binaries fire custom logic after each successful clone/update — kglite-mcp-server will use this to invoke code_tree::build on the freshly-activated repo and pin the resulting graph.

• Self-contained ISO-8601 (seconds-precision) formatter avoids pulling in chrono for a handful of timestamps.

• End-to-end test: cloned rust-lang/rustlings from github.com, list_source returned the active repo’s tree, repo_management() listing shows it as [active] with access counts.

Phase 5 — Watch mode (--watch DIR). The CLI now spawns a recursive debounced filesystem watcher (default 500 ms debounce) that logs change events at INFO level and can fire a downstream-supplied callback on each batch. Source roots are auto-pinned to the watched directory so the source tools (read_source / grep / list_source) operate on the live tree. Powered by the notify + notify-debouncer-mini crates. Downstream binaries (kglite-mcp-server, etc.) plug in their rebuild logic via the ChangeHandler callback type — phase-6 work will wire one in for code-tree rebuilding once kglite layers in.

Phase 4 — Python extension layer. Embeds CPython into the binary via PyO3’s auto-initialize feature so manifest-declared python: tools and custom embedder factories work out of the box.

• Manifest tools: [{ name, python: ./X.py, function: F }] entries load via importlib.util (no sys.path mutation), introspect the function signature with inspect.signature to derive a JSON Schema for MCP, and register dynamically on rmcp’s tool router via ToolRoute::new_dyn so the agent sees them in tools/list alongside the built-in source / GitHub tools.

• Manifest embedder: { module, class, kwargs } block is loaded

  • instantiated at boot. The PyObject is held in memory; downstream binaries (kglite-mcp-server) wire it to a graph’s text-score path via their own integration.

• Two-signal trust gating: python: tools require both trust.allow_python_tools: true and --trust-tools; embedders require trust.allow_embedder: true + --trust-tools. Refusing either way is the default. Boot-time errors are clear and specific.

• Type-hint → JSON Schema mapping: str → string, int → integer, float → number, bool → boolean, list → array, dict → object. Unmatched annotations fall back to string with the Python repr in the schema’s title field. Defaults are JSON-encoded into default.

• ServerHandler impl on McpServer switched from Self::tool_router() (static) to self.tool_router (instance) so dynamic routes added before serving show up in tools/list.

• End-to-end test: a def greet(name: str, count: int = 3) -> str Python function loads, registers with the right schema (name required, count defaulted), and dispatches correctly through tools/call.

The FastMCP-API-compat shim (from mcp_methods.fastmcp import FastMCP) is deferred to a follow-up. The manifest form already accepts any plain Python function — users with existing FastMCP code just declare each decorated function as a separate manifest entry until the shim ships.

Phase 3 — GitHub tools (github_issues, github_api) registered on the rmcp server. Both tools resolve the active repo via a caller-supplied dynamic provider with an optional per-call repo_name= override; auto-detects from cwd’s git remote as a last resort. github_issues covers all three modes — FETCH (number=), SEARCH (query=), LIST (no args) — by delegating to the existing mcp_methods::github Rust internals (no PyO3 in the hot path). To make that delegation possible, mcp-methods now ships as both a Python extension (cdylib) and a regular Rust library (rlib), with the extension-module PyO3 feature gated behind the new python-extension Cargo feature so cargo build can produce both. pyproject.toml maturin features updated accordingly. End-to-end stdio test against github.com/rust-lang/rustlings confirmed.

Phase 2 — source tools (read_source, grep, list_source) registered on the rmcp server. Each tool is gated on the server having an active source-roots provider (static or dynamic); when none is configured, the tool returns a friendly “configure source_root in your manifest” error rather than crashing. Implementation lives in crates/mcp-server/src/source.rs and uses the same ignore + grep-matcher/grep-regex/grep-searcher crates as the existing mcp-methods primitives. ServerOptions gains with_static_source_roots

• with_dynamic_source_roots. Manifest source_root(s) are now canonicalised at boot and wired into the server. 15 new unit tests covering read/grep/list semantics, glob filtering, traversal blocking.

Phase 1 — bootstrap. Boots a working MCP server with the framework wired end-to-end, plus the manifest schema parsed and validated. No real tools yet — that’s phase 2+.

• Cargo workspace conversion of mcp-methods (root crate unchanged; crates/mcp-server/ added as a sibling member).

• YAML manifest parser at crates/mcp-server/src/manifest.rs — direct port of the Python kglite.mcp_server.manifest schema. Same keys (name, instructions, overview_prefix, source_root(s), trust.{allow_python_tools, allow_embedder}, tools, embedder, builtins.{save_graph, temp_cleanup}), same validation messages, same auto-detection of sibling (<basename>_mcp.yaml) and workspace-level (workspace_mcp.yaml) manifests.

• clap-based CLI matching the Python flags: --graph / --workspace / --watch (mutually exclusive), --mcp-config, --embedder, --name, --trust-tools, --stale-after-days.

• rmcp ServerHandler impl with one ping tool to verify the framework dispatch is wired. End-to-end stdio handshake confirmed (initialize → tools/list → tools/call).

• 25 unit tests covering manifest parsing edge cases and CLI mode picking.

0.3.19

• Built-in html_to_text function — converts HTML to clean, readable text optimized for LLM consumption. Strips <head>, <script>, <style>, and comments. Converts headings to markdown # prefixes, list items to - bullets, bold/strong to **text**, images to [image: alt], tables to tab-separated text, and links to plain text. Decodes 75+ named HTML entities (including Scandinavian æøå) plus numeric/hex references. Available as a standalone function (from mcp_methods import html_to_text) and as a string-based transform on read_file (transform="html").

• String-based transform on read_file — transform now accepts "html" in addition to callables. The built-in html transform runs after section extraction (so id attributes remain available) but before grep (so patterns match clean text, not raw tags). Callable transforms preserve existing behaviour.

0.3.17

• Neutral error for non-existent items — fetching a number that doesn’t exist as an Issue, PR, or Discussion now returns #N not found in repo (checked Issues, PRs, and Discussions) instead of leaking the GraphQL fallback error ("Could not resolve to a Discussion").

0.3.16

• Renamed github_discussions → github_issues — one tool, three modes: FETCH (by number), SEARCH (by query), LIST (default). github_discussions remains as a backward-compat alias.

• Search mode — query="datatree coordinates" searches via REST search/issues for issues+PRs, and GraphQL search(type: DISCUSSION) for Discussions. kind routes to the right API; kind="all" runs both and concatenates results. Sort defaults to relevance for search, "created" for listing.

• Renamed ElementCache.fetch_discussion → fetch_issue.

• labels parameter simplified — now a comma-separated string ("bug,P0") instead of Vec<String>.

• sort parameter now optional — defaults depend on mode: None (relevance) for search, "created" for listing.

0.3.15

• GitHub Discussions support (GraphQL) — fetch_discussion and github_discussions now transparently handle GitHub Discussions, not just Issues and PRs. When a REST lookup returns 404, the library falls back to the GraphQL API to fetch the Discussion with full threaded comments (top-level + nested replies), category, and answered status. Listing mode supports kind="discussion" to query Discussions via GraphQL with state and sort filtering. Ref collection also extracts GitHub references from threaded reply bodies.

0.3.14

• max_matches parameter for read_file grep — limit the number of matches returned when grepping within a file. When a dense document has 125 hits, max_matches=20 returns the first 20 with context, and the header changes to “showing 20 of 125 matches”. The ripgrep module already had max_results/match_limit; this brings the same control to single-file grep. Also improved truncation footers: when max_chars cuts grep output, the footer now includes the total match count (e.g., “125 matches, 279865 chars total”) so you know whether to refine the pattern or increase the limit.

0.3.13

• grep parameter for read_file — search within a single file and return only matching lines with context. Avoids reading entire large documents into context when only specific passages are needed. Supports grep_context (default 2) for surrounding lines, merges overlapping context windows, works with section, start_line/end_line, transform, and max_chars. Uses -- separators between non-contiguous match groups, consistent with ripgrep output.

0.3.12

• UTF-8 fix for section extraction — the byte-stepping loop panicked on multi-byte characters (§, æ, ø, å, é, etc.) inside extracted sections. Now advances by full UTF-8 codepoints. Also hardened all max_chars truncation sites to avoid splitting multi-byte characters.

0.3.11

• section parameter for read_file — extract an HTML element by its id attribute. Solves single-line HTML navigation: instead of getting 127KB on line 96, request section="PARAGRAF_4-7" to get just that element. Infers tag name from the matched opening tag, handles nested elements of the same type, works with transform and max_chars.

0.3.10

• Comment TOC — bare element_id="comments_middle" returns a lightweight table of contents (_index, author, created_at, 80-char snippet) instead of dumping raw JSON.

0.3.9

• lines on array elements — lines="1-20" on comments_middle returns structured comment objects by index range.

• _index on highlights — maintainer highlights include _index for drill-down.

• Grep metadata on comments — grep matches include author, created_at, comment_index, and element_id.

0.3.7

• Thread digest — discussions with 50+ comments are condensed: first 5 + maintainer highlights + last 5 inline, middle cached as comment_N and searchable comments_middle.

• Bookend pagination — fetches first 5 + last 5 comment pages, skipping the middle. Prevents freezing on huge threads.

• Lazy related refs — cross-references listed as related_refs instead of eagerly fetched.

• Unicode safety — fixed byte-slicing panics on multi-byte UTF-8 characters.

0.3.6

Improvements

• Budget-based adaptive compaction — fetch_discussion / compact_discussion now start with full content and only compact what’s needed to fit within a byte budget (default 60KB). Small/medium PRs return fully expanded with no user effort. Large PRs gracefully degrade through 9 progressive tiers (bot filter → code blocks → comments → large patches → body → reviews → all patches → aggressive).

• Removed expand parameter — no longer needed. Compaction is fully automatic based on size constraints. Compacted content is always available via element_id drill-down.

• Per-item budget (default 15KB) prevents any single patch, comment, or body from consuming more than 25% of the total budget, ensuring balanced output even when one file dominates a PR.

• budget / item_budget parameters on compact_discussion for power users who want to tune output size.

• _compaction metadata in output describes what was compacted and at which tier, so callers know what to drill into.

0.3.5

Improvements

• Smart diff sizing — small PR diffs (≤200 total lines) are shown inline with per-file collapsing for large individual patches. Large diffs show a navigation tree with +/- counts; drill into specific files via element_id="patch_N". All patches are always cached regardless of size.

• Review comments as review_N cache elements — inline review comments are now individually drillable via element_id="review_3" with grep and lines support. Previews extended from 1 line/120 chars to 3 lines/300 chars.

0.3.4

Fixes

• list_dir annotate callback paths — the callback now receives paths relative to relative_to (e.g. src/core/engine.py) instead of bare filenames (engine.py). This was a bug that made it impossible to match callback paths against external data sources (knowledge graphs, databases) when listing subdirectories.

0.3.3

Improvements

• PR diffs as collapsed cache elements — when fetching a PR via ElementCache.fetch_discussion, diff patches are automatically collapsed into patch_N cache elements. Each stores filename, additions/deletions, and full diff text. Drill into specific files with element_id="patch_3", search within patches with grep="pattern", or slice with lines="10-30". Fits the existing progressive-disclosure pattern alongside cb_N, comment_N, and details_N.

• refresh flag on fetch_discussion — subsequent calls for the same (repo, number) now return a cached summary instead of re-fetching. Pass refresh=True to force a fresh fetch when the discussion has changed.

• Removed git_diff — PR diffs are better served as collapsed elements in fetch_discussion (progressive disclosure). For comparing tags/branches outside a PR context, use git_api("compare/v1.0...v2.0").

• Removed globset direct dependency (was only used by git_diff)

0.3.2

Improvements

• git_diff GitHub API fallback — when local git diff fails (shallow clones, missing refs), automatically falls back to the GitHub compare API (/repos/{repo}/compare/{base}...{head}). Repo is auto-detected from git remote or can be passed explicitly via the new repo parameter.

0.3.1

Fixes

• Fixed CI import check referencing removed git_issue export

• Fixed stale git_issue reference in ElementCache error message

0.3.0

Breaking changes

• Renamed head_limit → max_results across the API. In ripgrep(), the parameter is now max_results. In ripgrep_files(), the old max_results (engine-level early termination) is now match_limit, and head_limit (output truncation) is now max_results.

• Renamed git_issue → github_discussions. Now supports both fetching a single discussion and listing discussions with filters.

• Renamed ElementCache.fetch_issue → ElementCache.fetch_discussion.

New features

• github_discussions listing mode — list issues, PRs, or both with kind, state, sort, limit, and labels filters. Auto-detects repo from git remote when repo is omitted.

• list_dir annotate callback — optional annotate parameter accepts a callable that receives each entry’s relative path and returns an annotation string (e.g. "(144 loc)"). The tree formatter handles column alignment within each directory level.

0.2.11

New features

• list_dir — tree-formatted directory listing with depth control, glob filtering, .gitignore support, directory summaries, and relative_to for path display.

Performance optimizations

• Eliminated double filesystem walk in list_dir (merged into single walk at depth+1)

• Replaced HashSet+sort+dedup with O(n) sorted merge for context line merging in grep

• Thread-local buffering with FlushGuard Drop pattern in parallel walker (one lock per thread instead of per file)

• Thread-local single-entry regex cache in json_grep and cache modules

• Pre-canonicalize allowed_dirs in read_file to reduce filesystem stat calls

• eq_ignore_ascii_case() replacing .to_lowercase() allocation in HTML tag detection

• LazyLock<HashSet<&'static str>> for zero-allocation default skip directories

0.2.10

Bug fixes

• Fixed head_limit semantics: changed from int (0 = unlimited) to int | None (None = unlimited)

• Added relative_to parameter to ripgrep() wrapper

0.2.9

Bug fixes

• Removed default max_results limit that silently truncated search results

0.2.8

Changes

• Renamed all grep methods to ripgrep across the codebase

• Dropped deprecated macos-13 CI runners from wheel build workflow

• Removed tracked __pycache__ files from git

0.2.7

Changes

• Fixed wheel build workflow for cross-platform distribution

0.2.5

Improvements

• Searcher reuse in transform (callback) path — build searcher and sink once, reuse across files

• Fast path for no-context matches in format_content (skip HashSet/sort/dedup)

• Context merge moved inside the context branch to avoid allocation when unused

0.2.3

Major rewrite — Rust conversion

• Rewrote core from pure Python to Rust via PyO3/maturin

• grep: Uses grep-regex, grep-searcher, and ignore crates (parallel file walking, mmap, SIMD literal optimization, .gitignore support)

• GitHub integration: git_issue, git_api, ElementCache with drill-down caching, text compaction

• File I/O: read_file with path traversal protection

• Compaction: compact_discussion, collapse_code_blocks, compact_text

• Added ripgrep() Claude Code Grep-compatible wrapper

• Added CI (cargo fmt, clippy, pytest) and wheel build workflows

0.1.1

• Packaging fix

0.1.0

• Initial release — pure Python implementation