rubik 0.1.0

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data/ATTRIBUTION.md

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+# 📜 Open Source Attributions & Third-Party Notices
+
+Rubik is built on the shoulders of giants. This document acknowledges and credits the open-source projects, academic research, and engineering communities whose code, ideas, and tools made Rubik possible.
+
+---
+
+## 🍴 1. Forked & Ported Projects
+
+### bash-classify
+- **Original Project:** [`bash-classify`](https://github.com/fprochazka/bash-classify)
+- **Original Author:** Filip Procházka ([@fprochazka](https://github.com/fprochazka))
+- **Original Language:** Python
+- **License:** MIT License
+- **Rubik Integration:**
+  - Ported to pure Ruby under [`lib/rubik/security/classifier/`](lib/rubik/security/classifier/).
+  - Includes the comprehensive command database (175 popular CLI tool definition YAML files under [`lib/rubik/security/classifier/commands/`](lib/rubik/security/classifier/commands/)).
+  - Adapted to use `tree-sitter` for AST parsing, and extended with first-class **PowerShell** (`pwsh`) cmdlet risk classification and execution policy checking.
+
+```
+MIT License
+
+Copyright (c) 2025 Filip Prochazka
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+---
+
+## 🏛️ 2. Theoretical & Architectural Foundations
+
+### Spatiotemporal Composability
+- **Paper:** *"A Programming Paradigm for Spatiotemporal Composability"*
+- **Authors:** Yifan Shi (Peking University, DeepSeek-AI), Wei Zhang (Peking University), Tianyi Cui (DeepSeek-AI)
+- **Reference Architecture:** Cordis / Cordiverse Meta-Framework
+- **Rubik Implementation:**
+  - Theoretical backbone codified in [`AGENTS.md`](AGENTS.md).
+  - **Temporal Composability:** Monoidal LIFO Inverse Accumulator ($\Omega$) implemented in [`Rubik::Runtime::Context`](lib/rubik/runtime/context.rb).
+  - **Spatial Composability:** Reactive Coeffect Dependency DAG ($\Sigma \vdash C : \tau$) implemented in [`Rubik::Runtime::ComponentFiber`](lib/rubik/runtime/fiber.rb) and [`Rubik::Runtime::Manager`](lib/rubik/runtime/manager.rb).
+  - Zero-downtime hot reloading, atomic rollback on activation failure, and leak-free lifecycle management.
+
+---
+
+## 🌳 3. AST Parsing & Multi-Language Ecosystem
+
+### Tree-sitter
+- **Project:** [`tree-sitter`](https://github.com/tree-sitter/tree-sitter)
+- **Authors:** Max Brunsfeld and the Tree-sitter Authors
+- **License:** MIT License
+- **Usage:** Fast, incremental, robust concrete syntax tree parsing for multi-language semantic code intelligence, symbol extraction, and command security analysis.
+
+### tree_sitter_language_pack
+- **Project:** [`tree-sitter-language-pack`](https://github.com/xberg-io/tree-sitter-language-pack)
+- **Maintainer:** xberg-io
+- **License:** MIT License
+- **Grammars Leveraged:**
+  - `tree-sitter-bash`
+  - `tree-sitter-powershell`
+  - `tree-sitter-ruby`
+  - `tree-sitter-python`
+  - `tree-sitter-go`
+  - `tree-sitter-rust`
+  - `tree-sitter-c`
+  - `tree-sitter-zig`
+  - `tree-sitter-typescript` / `tree-sitter-javascript`
+
+---
+
+## 🛡️ 4. Operating System Sandboxing & Isolation
+
+### Bubblewrap (`bwrap`)
+- **Project:** [`bubblewrap`](https://github.com/containers/bubblewrap)
+- **Authors:** Project Atomic / Flatpak / GNOME contributors
+- **License:** LGPL-2.0-or-later
+- **Rubik Integration:**
+  - [`Rubik::Sandbox::Driver::BubblewrapDriver`](lib/rubik/sandbox/driver/bubblewrap.rb) utilizes unprivileged user namespaces (`CLONE_NEWUSER`, `CLONE_NEWNET`, `CLONE_NEWPID`) for hardware-enforced filesystem and network confinement without requiring root privileges.
+
+### Container Runtimes (Docker & Podman)
+- **Projects:** [`moby/moby` (Docker Engine)](https://github.com/moby/moby) · [`containers/podman`](https://github.com/containers/podman)
+- **Licenses:** Apache-2.0 (Docker/Moby) · GPL-2.0-or-later (Podman; libpod)
+- **Rubik Integration:**
+  - [`Rubik::Sandbox::Driver::DockerDriver`](lib/rubik/sandbox/driver/docker.rb) and [`Rubik::Sandbox::Driver::PodmanDriver`](lib/rubik/sandbox/driver/podman.rb) drive these engines as **external CLI tools only** (no source code incorporated): workspace bind-mounts, memory/CPU/pids limits, and default network-off confinement.
+  - [`Rubik::Sandbox::Driver::ProcessDriver`](lib/rubik/sandbox/driver/process.rb) provides the always-available direct host fallback when no kernel-level sandbox is present.
+
+---
+
+## 💎 5. Open Source Ruby Gems & Libraries
+
+| Gem | Author / Maintainer | License | Role in Rubik |
+| :--- | :--- | :--- | :--- |
+| **`diff-lcs`** | Austin Ziegler | MIT / Artistic / GPL | Longest Common Subsequence unified diff generation and hunk merging ([`Rubik::Buffer::Diff`](lib/rubik/buffer/diff.rb)). |
+| **`tty-prompt`** | Piotr Murach | MIT | Interactive command-line select dialogs, multi-choice prompts, and questionnaires. |
+| **`tty-spinner`** | Piotr Murach | MIT | Managed non-blocking lifecycle spinners and progress indication. |
+| **`tty-markdown`** | Piotr Murach | MIT | Terminal ANSI/colorized Markdown rendering in the interactive REPL. |
+| **`tty-which`** | Piotr Murach | MIT | Cross-platform executable binary locator. |
+| **`pastel`** | Piotr Murach | MIT | Clean, chainable ANSI terminal coloring and theme painting. |
+| **`strings-ansi`** | Piotr Murach | MIT | ANSI-aware string truncation and alignment for REPL formatters. |
+| **`reline`** | Hiroshi SHIBATA & Ruby Team | Ruby License / BSD-2-Clause | Line-editing, history navigation, autocompletion hooks, and headless terminal adaptation. |
+| **`prism`** | Kevin Newton & Ruby Core Team | MIT | High-performance Ruby parsing and AST extraction ([`Rubik::AST::RubyExtractor`](lib/rubik/ast/ruby_extractor.rb)). |
+| **`minitest`** | Ryan Davis & seattlerb | MIT | Fast, modular test suite powering Rubik's 1,690+ unit, integration, and contract tests. |
+| **`rubocop`** | Bozhidar Batsov & contributors | MIT | Static code analysis, style enforcement, and architectural hygiene gates. |
+| **`benchmark`, `logger`, `pstore`, `reline`, `fiddle`** | Ruby core / rubygems teams | Ruby License / BSD-2-Clause | Ruby stdlib gems pinned explicitly in `rubik.gemspec` as they are unbundled from the default set in Ruby 3.4/3.5. |
+
+---
+
+## 🌐 6. Industry Specifications & Open Protocols
+
+- **Language Server Protocol (LSP):**
+  - Specification by Microsoft Corporation (licensed under MIT / CC BY 4.0).
+  - Powering Rubik's cross-language diagnostics, symbol outlines, and jump-to-definition.
+- **Model Context Protocol (MCP):**
+  - Specification and reference architecture by Anthropic, PBC (licensed under MIT License).
+  - Powering Rubik's dynamic multi-server tool discovery, stdio transport, and spatiotemporal tool isolation.
+- **Server-Sent Events (SSE):**
+  - W3C Recommendation standard for streaming real-time LLM token responses and event telemetry.
+- **Semantic Versioning 2.0.0:**
+  - Specification by Tom Preston-Werner (CC BY 3.0).
+
+---
+
+## ⚖️ 7. License of Rubik
+
+Rubik itself is licensed under the **MIT License**.  
+See the [`LICENSE`](LICENSE) file for the full license text.

data/CHANGELOG.md

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+# Changelog
+
+All notable changes to Rubik are documented here. 0.1.0 is the first packaged
+release; its section is the thematic roll-up of the pre-gem history (485
+commits, 2026-08-23 → 2026-10-09, see `git log`).
+
+The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
+
+## Unreleased
+
+### Added
+
+- **Vakanüvis recall + write hardening** (issues #99/#100): `storage put`
+  now rejects non-string tags instead of silently stringifying booleans
+  into tag lists; search folds queries and haystacks with a Turkish-aware
+  I-class rule (ı/İ now match ASCII I text both ways) and ranks matches
+  with a deterministic field-tier bonus (title > tags > body, BM25 still
+  primary); an empty keyword-AND recall degrades honestly — top-3
+  OR-relaxed fallback matches plus a matching-transcript count hint;
+  `record` accepts first-class `tags` and deterministically auto-repairs
+  a missing `Keywords:` line; `forget` retires note refs (annal.*)
+  besides memory cards; digest compiles supersede byte-identical or
+  same-title duplicate pages instead of opening twins; a manual wiki
+  delete rebuilds the home index immediately; and two new chronicler
+  actions — `topics` (cold-start orientation over recorded cards) and
+  `digest_status` (queued vs in-flight digest visibility).
+
+- **Structured goal ledger** (`orchestrator/goal_ledger/`, `goal.ledger.*`,
+  default ON — SKILL.state adaptation): the `!goal` loop now keeps a
+  rev-guarded ΔΣ state ledger (objective, tasks, findings, decisions,
+  open questions, environment notes) that the maestro patches through the
+  root-only `update_goal_ledger` tool (RFC 6902 subset; classified
+  `syntax/schema/conflict` feedback with a bounded retry budget). The
+  current Σ is pinned through every compaction tier and re-injected each
+  step; every accepted revision appends a storage row (`goal-ledger`
+  ref). Re-verification (`goal.ledger.verify`): declarative FS verify
+  specs are re-checked at step boundaries — failures flip tasks to
+  `stale` via an internal rev-bumping mutation (a stale-rev `:conflict`
+  is the drift signal) and ride a silent `:ledger_drift` event plus a
+  bounded drift note. Observation projection
+  (`goal.ledger.observe_projection`): at compaction time, banked tool
+  results get per-row `<absorbed_into_ledger>` tombstones (rows are
+  never dropped; the last `observe_window` turns stay raw). All three
+  knobs ship ON with explicit opt-out; `goal.*` config is operator-only.
+
+- **Context pruner** (`repl/pruner/`, via `subagents.pruner.*` — shipped
+  DEFAULT OFF on 2026-10-09, then enabled by DEFAULT on 2026-10-10, see
+  Changed below):
+  a semi-deterministic cleaner for the ROOT (maestro) conversation window,
+  modeled on the Vakanüvis two-plane design. An LLM "Context Pruner"
+  subagent proposes a keep/drop/summarize plan from a deterministic unit
+  snapshot; the harness validates it against strict invariants (goal
+  pinning, tool-use pairing, head/tail bands, target token budget) and
+  applies it atomically at the next turn boundary — never mid-turn, never
+  from a background thread. Surfaces: the `prune_context` tool
+  (root-only, coeffect-gated, invisible while the knob is off), the
+  `!prune [now|status]` command, auto-scheduling on `:turn_finished`
+  gated by `trigger_ratio`/`min_turns_between`. The deterministic
+  compaction stack is unchanged and remains the safety net; subagent
+  pruning stays fully deterministic and untouched.
+
+### Changed
+
+- **The root window pruner is enabled by default** (`subagents.pruner.enabled`
+  `false` → `true`, 2026-10-10 user decision). Every root session now boots the
+  pruner harness: the `prune_context` tool and `!prune` command are on, and the
+  LLM pruner auto-fires at `trigger_ratio` once the window estimate crosses it
+  (budget still bounded by `max_steps`/`min_turns_between`; the deterministic
+  compaction stack remains the safety net and subagent channels stay untouched).
+  The knob remains as an explicit opt-out kill-switch
+  (`subagents.pruner.enabled: false`); the `RUBIK_TEST=1` suite armor is
+  unchanged, so scripted tests keep the pruner unbound unless
+  `RUBIK_PRUNER_FORCE=1`.
+
+- **Subagent transcript health package**: the durable subagent transcript
+  is now an operational log, not a verbatim history dump. (1) The runtime-
+  assembled system prompt (history row 1) serializes as a meta stub —
+  `[assembled system prompt omitted] prompt_sha256=<first 16 hex>` — for
+  builtin archetypes, whose prompts are reconstructible from defaults;
+  custom types (`synthesize_tool`) and caller-provided `system_prompt:` keep
+  the verbatim copy, since they are the single record anywhere. A frozen
+  prompt blob was a config+version derivative with neither recorded;
+  the provenance hash makes it verifiable and drift-detectable instead.
+  (2) Redaction parity with root session logs: every durable row passes the
+  same `Rubik::Security::Redactor` masker (text patterns + secret-shaped
+  keys), so a secret echoed in tool output or args no longer lands raw in
+  the storage-absorbed transcript; in-memory history stays raw for provider
+  wire fidelity. (3) Transcript index entities are task+result centric
+  instead of "first 40 JSONL lines": system-prompt boilerplate no longer
+  pollutes the BM25 corpus and the final result is now searchable ("which
+  subagent reported red?"); failed instances still get a body (task + state
+  line) and the upsert/dedupe/canonical-link contract is unchanged.
+
+### Fixed
+
+- **REPL wake-loop**: subagent notices stranded at turn end re-armed the
+  reactive wake (synthetic Enter), so a steady subagent stream chained
+  autonomous maestro turns forever — the prompt never returned and the cycle
+  survived Ctrl+C, because the interrupted turn's own ensure block re-armed
+  the wake. Settlement invariant: an autonomous notice turn never spawns
+  another one, and an interrupted turn settles the wake debt; the
+  model-channel no-loss delivery is unchanged.
+
+## [0.1.0] - 2026-10-09
+
+First rubygems.org release of the `rubik` gem. Linux and macOS install out of
+the box; **Windows** needs the Rust GNU toolchain because
+`tree_sitter_language_pack` publishes no Windows prebuilt — see the README
+installation section.
+
+### Added
+
+- **Vakanüvis v2 pipeline** (plan `_plan/vakanuvis-v2-2026-10-06.md`, from the
+  vue-hakedis review `note.2.6af8197f2600ea57`): the chronicler's compile
+  pipeline is now card-first and recall-aware.
+  - `Store#search_ranked` — BM25-lite relevance ranking for recall (same
+    token-AND candidate gate as `search`; df free from the filter pass,
+    bytesize length normalization, tf scanned only over matches; ties break
+    `updated_at` desc then `[type,row]`). `search`'s `[type,row]` contract is
+    untouched; ranking lives in the recall presentation layer only. New rake
+    bench metric measures the ranked/plain add-on ratio (1.44x measured).
+  - Card-first distiller brief: memory cards head the source list (capped,
+    honest empty state), the session annal is demoted to an event index, and
+    the content policy bans "turn N" narratives/raw measurements, requires a
+    one-sentence opener (doubles as the home-index line), `Last verified:`,
+    and a bilingual `Keywords:` line (recall is keyword-AND; a TR query
+    cannot find an EN page without shared vocabulary). Harvest stamps
+    `links['verified_session']` as the deterministic staleness trace.
+  - Source discipline: `job[:transcript_uris]` (previously declared but never
+    populated) now snapshots completed-only, non-vakanuvis transcripts
+    (newest 8); the brief fences the list as out-of-scope beyond it.
+  - Recall smoke test: proposals may end with up to 5 `CHECK: <query>` lines;
+    the harness runs them through real recall semantics after each compile,
+    writes recall-gap note cards on misses, surfaces them in the next brief
+    as Keywords-enrichment requests, and supersedes the gap note on a clean
+    pass (self-healing; Plane 1 never edits distilled prose).
+  - Dirty-guarded batch spawning (durable-content footprint instead of raw
+    event counts — pure turn traffic no longer burns a distiller) and digest
+    dedupe ("already queued" receipt for in-flight targets). The wiki home
+    index now carries a one-line summary per page.
+
+### Changed
+
+- **Storage reads are UTF-8-pinned and cached**: store file reads
+  (`load_records`, meta/index, transcript excerpts) force UTF-8 with scrub
+  instead of trusting the process external encoding — non-ASCII recall
+  queries no longer risk `Encoding::CompatibilityError` on non-UTF-8 Windows
+  locales (TR cp1254/cp857). `Store#search`/`list` accept a type ARRAY,
+  and parsed records plus search haystacks are memoized behind an
+  mtime-validated cache (writes drop it; external edits self-heal). Measured
+  123 ms → 14 ms per warm scoped query on a synthetic 1150-row/1 MB store.
+
+- **Silent concurrency via Fiber Scheduler** (`Rubik::Concurrency`): a
+  pure-stdlib `Fiber::Scheduler` event loop (`IO.select` + monotonic timer
+  heap + self-pipe cross-thread wakeups) with a thread-scoped `silently` /
+  `map(enum, concurrency:)` boundary. Plain blocking I/O call sites —
+  Net::HTTP, sleep backoffs, Open3 pipe reads/writes, Mutex/CV waits,
+  Thread#join — interleave cooperatively on one thread with ZERO changes at
+  the call sites (thousands of concurrent ops; I/O concurrency, not CPU
+  parallelism). Handles the Ruby 3.3/4.0 scheduler protocol drift
+  (`fiber(&blk)` creation handoff, io_read/io_write buffer contracts) and
+  Windows realities (no `IO#nonblock=`; `Fiber.blocking`-wrapped
+  nonblocking primitives). Escape hatch: `RUBIK_FIBER_SCHEDULER=off`
+  degrades every boundary to sequential execution.
+
+- **MCP config boot overlaps server connect phases**:
+  `Manager#load_from_config` now runs the slow I/O half (spawn +
+  initialize + tools/list) of every configured server concurrently through
+  the concurrency boundary while registration and state application stay
+  sequential in config order. Boot wall clock goes sum(per-server) →
+  max(per-server); one hung server no longer delays the rest. Per-server
+  failure isolation, warning text, and tool registration order are
+  byte-identical to the sequential path (`RUBIK_FIBER_SCHEDULER=off`
+  restores it). Tests can inject fakes via `Manager.new(client_factory:)`.
+
+### Highlights
+
+- **Self-evolving tool runtime**: synthesized tools with fail-closed AST
+  security gates, hot reload, and unsynthesize; skills and MCP tools join the
+  same coeffect-gated registry.
+- **Spatiotemporal runtime**: revertible-effect `Context` (LIFO Ω unwind,
+  atomic rollback, deferred-signal drain), topological fiber reconciliation,
+  reactive provide/unprovide, and a kernel event bus with dmesg telemetry
+  (Plans 102–107).
+- **Subagent hierarchy**: init-0 orchestration contexts, step budgets with
+  pause/resume negotiation, wait protocol with reactive event-bus wakeups,
+  process-unique transcript ids, and budget transparency (Plans 94–96, 109).
+- **Security gate hardening**: command classifier with fail-closed unknown
+  handling, symlink-resolved critical-write block, TOCTOU-closed atomic
+  writes, unified guard policy, secret redaction, and sandbox process
+  isolation (Plan 108, 111).
+
+### Added
+
+- Agent loop: token budget autonomy with auto-continuation, wait hints,
+  reactive wakeups, and structured failure notices (Plan 90, 109).
+- Kernel: deterministic event dispatcher, kworker queue, monotonic dmesg ring
+  buffer with `!dmesg` (Plans 102–104).
+- Tools: `ask_question` interactive dialog (Plan 92), async background task
+  manager with `manage_task` (Plan 93), native search with rg fallback,
+  AST-backed symbols, LSP diagnostics surfacing.
+- REPL: `!paste` mode with burst join (Plan 91), per-dispatch CommandContext,
+  session prune, command usage synopses, non-blocking prompt with terminal
+  guard (Plan 105).
+- Config: typed model/provider catalog CRUD (`upsert_provider_model`,
+  `set_model_spec`, …) with uniform persist-failure outcome hashes; modular
+  Config (defaults/deep_ops/store/model_catalog mixins).
+- Testing: shared scripted agent-loop harness, slow-file quarantine with
+  measured profiling, parallel worker task (N=4 stable).
+
+### Fixed
+
+- Security: classify env-assignment payloads as inner commands; expression-
+  exclusive dangerous-AST sentinel; normalize paths and canonicalize Windows
+  allowlists; keep delegated redirects classified.
+- Runtime: per-fiber dispose isolation with LIFO unwind; complete context
+  drain before re-raising interrupts; post-dispose registration guard;
+  task-tree teardown via `kill_all` inverse.
+- LLM: jittered retries, idle-reset stream timeouts, honest blocked-guidance
+  reasons, overflow-pattern hardening.
+- Buffer: resolved containment enforced at both sanitize and apply
+  boundaries; rename-only atomic writes; apply-failure surfacing.
+- LSP: robust header framing with response TTL and cancellation; Windows byte
+  framing; reader-loop error isolation.
+- Config/REPL: silent-persist gaps closed — blocked deletions surfaced,
+  persist failures reported instead of silent success.
+
+### Performance
+
+- AST: sub-second mtime plus content-hash cache keys; persistent lazy
+  indexing (Plan 39); background warmup with teardown joins.
+- Context: serialized index mutations, snapshot-outside-lock reconcile,
+  streaming-first truncation.
+
+[Unreleased]: https://github.com/ozgurulukir/rubik/compare/v0.1.0...HEAD
+[0.1.0]: https://github.com/ozgurulukir/rubik/releases/tag/v0.1.0

data/LICENSE

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+MIT License
+
+Copyright (c) 2026 Özgür Ulukır, Rubik Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.