chore(deps): bump the root-npm-minor-patch group with 3 updates

Bumps the root-npm-minor-patch group with 3 updates: [@cline/sdk](https://github.com/cline/cline/tree/HEAD/sdk/packages/sdk), [@modelcontextprotocol/inspector](https://github.com/modelcontextprotocol/inspector) and [cline](https://github.com/cline/cline/tree/HEAD/apps/cli). Updates `@cline/sdk` from 0.0.41 to 0.0.54 - [Release notes](https://github.com/cline/cline/releases) - [Changelog](https://github.com/cline/cline/blob/main/CHANGELOG.md) - [Commits](https://github.com/cline/cline/commits/sdk/sdk/v0.0.54/sdk/packages/sdk) Updates `@modelcontextprotocol/inspector` from 0.21.2 to 0.22.0 - [Release notes](https://github.com/modelcontextprotocol/inspector/releases) - [Commits](https://github.com/modelcontextprotocol/inspector/compare/0.21.2...0.22.0) Updates `cline` from 3.0.29 to 3.0.33 - [Release notes](https://github.com/cline/cline/releases) - [Changelog](https://github.com/cline/cline/blob/main/apps/cli/CHANGELOG.md) - [Commits](https://github.com/cline/cline/commits/cli-v3.0.33/apps/cli) --- updated-dependencies: - dependency-name: "@cline/sdk" dependency-version: 0.0.54 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: root-npm-minor-patch - dependency-name: "@modelcontextprotocol/inspector" dependency-version: 0.22.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: root-npm-minor-patch - dependency-name: cline dependency-version: 3.0.33 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: root-npm-minor-patch ... Signed-off-by: dependabot[bot] <support@github.com>
2026-08-13 10:30:35 +00:00 · 2026-06-29 14:47:51 +00:00
3 changed files with 218 additions and 490 deletions
--- a/MODULE_DECOMPOSITION.md
+++ b/MODULE_DECOMPOSITION.md
@ -1,273 +0,0 @@
-# Research-Stack MODULE_DECOMPOSITION.md
-
-**Date:** 2026-07-08
-**Status:** Analysis complete — 12 proposed standalone modules
-
---
-
-## Current State
-
- **Total .lean files:** 925 (in `0-Core-Formalism/lean/Semantics/`)
- **Sorry count:** 76 across 29 files
- **Foundation:** `Semantics.FixedPoint` imported by 452 files
- **Second layer:** `Semantics.Bind` imported by 71 files
- **Third layer:** `Semantics.DynamicCanal` imported by 25 files
- **Current lakefile:** `lakefile.toml` (monolithic, all roots in one target)
-
---
-
-## Proposed Module Groups (12 modules)
-
-### Module 1: `rs_core` — Foundation Axioms
-**Files:** 3 | **Sorry:** 19 | **External deps:** Mathlib (Manifold, Probability, Analysis)
-
-| File | Path |
-|------|------|
-| BindAxioms | Core/ |
-| InformationManifold | Core/ |
-| T1_Coherence | Core/ |
-
-**Internal deps:** None (this is the root)
-**Notes:** 19 sorrys in T1_Coherence (12) and InformationManifold (7). These are the "brain" — the SIM framework axioms. T1_Coherence v2.0 replaced vacuous `True := by trivial` with honest `sorry`.
-
---
-
-### Module 2: `rs_numerics` — Fixed-Point & Q16_16 Arithmetic
-**Files:** ~15 | **Sorry:** 0 | **External deps:** Mathlib (Data.Nat, Data.Int, Data.Real)
-
-Core files (imported by 452+ others):
- FixedPoint (the single most imported file)
- Q16_16Numerics
- Toolkit
- PhysicsScalarBridge
- RegimeCore
-
-**Internal deps:** rs_core (BindAxioms)
-**Notes:** This is the true foundation — almost everything imports FixedPoint. Must be extracted first.
-
---
-
-### Module 3: `rs_bind` — Bind Infrastructure
-**Files:** ~20 | **Sorry:** 0 | **External deps:** Lean.Data.Json, Mathlib
-
-Core files:
- Bind (imported by 71 files)
- DynamicCanal (imported by 25 files)
- LocalDerivative
- OrthogonalAmmr
- ManifoldStructures
-
-**Internal deps:** rs_core, rs_numerics
-**Notes:** Bind and DynamicCanal are the infrastructure layer that most domain modules depend on.
-
---
-
-### Module 4: `rs_braid` — Braid Theory
-**Files:** ~13 | **Sorry:** 0 | **External deps:** Mathlib
-
-Files (prefix `Braid*`):
- BraidBracket, BraidStrand, BraidCross, BraidField, BraidStateN
- BraidEigensolid, BraidSpherionBridge
- + related files
-
-**Internal deps:** rs_numerics, rs_bind
-**Notes:** Self-contained cluster with 22 internal imports. Clear boundary.
-
---
-
-### Module 5: `rs_physics` — Physics & Conservation Laws
-**Files:** ~30 | **Sorry:** 1 | **External deps:** Mathlib (Analysis, Topology)
-
-Subdirectories: `Physics/` (24), `PhysicsData/` (1), `FNWH/` (4)
-Key files:
- Conservation, Boundary, Interaction, Projection
- BurgersBridge, BurgersPDE
- DESIInvariant, DESIModelProjection
- NBody, QCLEnergy, RydbergExperimentalTest
- LHCb_BToKStarMuMu (real LHCb data!)
-
-**Internal deps:** rs_numerics, rs_bind
-**Notes:** Contains actual experimental data references (LHCb). The BurgersPDE files are imported by 13 others.
-
---
-
-### Module 6: `rs_extensions` — Biological & Ecological Extensions
-**Files:** 105 | **Sorry:** 0 | **External deps:** Mathlib (Analysis, SpecialFunctions)
-
-All files in `Semantics/Extensions/`:
- Biological laws (70+ files: BioComplexSystems, CellularGrowthLaws, etc.)
- Ecological dynamics (EcologicalBehaviors, EcologicalNetworkDynamics, etc.)
- Evolutionary dynamics (EvolutionaryLandscapeDynamics, etc.)
- Cognitive/social dynamics (CognitiveLearningDynamics, SocialCognitiveDynamics, etc.)
- Physics-adjacent (HarmonicKinkPlasmaManifold, HyperbolicStateSurface, etc.)
-
-**Internal deps:** rs_numerics, rs_bind
-**Notes:** Largest module (105 files). Could be further split into Bio/Ecology/Evolution/Cognitive sub-modules. Zero sorrys — these are all statement-only (axiom/theorem definitions without proof obligations).
-
---
-
-### Module 7: `rs_hcmmr` — HCMMR Laws & Kernels
-**Files:** 20 | **Sorry:** 0 | **External deps:** Mathlib
-
-All in `Semantics/HCMMR/`:
- Law14 through Law21 (Motion, SignalDetection, Field, Entropy, Observer, etc.)
- Kernels: HyperEigenSpectrum, BoundaryEigenFire, etc.
- FAMMScarMemory, SNRAnomalyDetector, PrimeGearCache
-
-**Internal deps:** rs_numerics, rs_bind
-**Notes:** Self-contained law framework. Clear naming convention (Law##).
-
---
-
-### Module 8: `rs_hardware` — Hardware & FPGA
-**Files:** 12 | **Sorry:** 0 | **External deps:** None (hardware-level)
-
-All in `Semantics/Hardware/`:
- AdaptiveFabric, AgenticHardware, BitstreamWitness
- Blitter6502OISC (OISC computer!)
- EmergencyBootShell/State/Types
- HardwareExtraction, LaserPathCell
- TangNano9K/ (3 files — actual FPGA target)
- NIICore, RGFlowFAMM
-
-**Internal deps:** rs_numerics
-**Notes:** Contains TangNano9K FPGA code. Self-contained hardware layer.
-
---
-
-### Module 9: `rs_nii` — NIICore Cognitive Architecture
-**Files:** 20 | **Sorry:** 0 | **External deps:** Mathlib
-
-All in `Semantics/NIICore/`:
- CognitiveLoadIntegration, DifferentialAttentionMorphing
- HierarchicalController, MetaLearning
- MorphicCoreId, MorphicFieldCategory, MorphingTriggers
- SemanticAnalysis, SemanticCapabilitySystem, SemanticRGFlow
- UncertaintyQuantification, Verification, etc.
-
-**Internal deps:** rs_numerics, rs_bind
-**Notes:** Self-contained cognitive architecture. Clear internal naming.
-
---
-
-### Module 10: `rs_genomic` — Genomic Compression
-**Files:** 6 | **Sorry:** 0 | **External deps:** Mathlib
-
-All in `Semantics/GenomicCompression/`:
- Components, Compression, Field, NonDriftProof, Theorems, Types
-
-Plus `Semantics/Biology/` (3 files):
- BioRxivFormalization, QuaternionGenomic, RGFlowBioinformatics
-
-**Internal deps:** rs_numerics, rs_bind
-**Notes:** Small, focused module. NonDriftProof name suggests drift-prevention guarantees.
-
---
-
-### Module 11: `rs_testing` — Tests & Benchmarks
-**Files:** ~45 | **Sorry:** 0 | **External deps:** Mathlib
-
- `Semantics/Testing/` (39 files): adversarial, baseline, conservation, GPU, benchmark tests
- `Semantics/Benchmarks/` (2 files): Grid17x17, HadwigerNelson
- `Semantics/Toybox/` (4 files): HierarchicalBinding, ObserverAngle, etc.
-
-**Internal deps:** rs_numerics (FixedPointTest, etc.)
-**Notes:** Test infrastructure. Should be buildable but not imported by other modules.
-
---
-
-### Module 12: `rs_scaffold` — Extension Scaffold
-**Files:** 36 | **Sorry:** 1 | **External deps:** Mathlib
-
-All in `ExtensionScaffold/`:
- **Compression/** (14 files): AdaptiveBlock, CellCore, CodingCost, HutterContext, etc.
- **Temporal/** (9 files): CommitClock, MetabolicTvi, OMT, RegenerationPolicy, etc.
- **ENE/** (5 files): SemanticLinter, SessionArchive, AutoImported, etc.
- **Physics/** (2 files): NBody, VideoWeirdMachine
- **Topology/** (2 files): PlasmaTopology, Wormhole
- **Thermodynamics/** (1 file): ThroatPhysics
- **Decoherence/** (1 file): HistoryTvi
- **Seed/** (1 file): uSeed
- MissingProofsTest (1 file)
-
-**Internal deps:** rs_numerics, rs_bind
-**Notes:** Already well-organized by subdirectory. Compression/ is the densest cluster.
-
---
-
-## Orphan / Unclassified Files
-
-These files in `Semantics/` (flat) don't clearly belong to any cluster:
-
-| File | Imports | Notes |
-|------|---------|-------|
-| SSMS | FixedPoint | Standalone |
-| ShellModel | FixedPoint | Standalone |
-| Canon | FixedPoint | Standalone |
-| GoldenSpiral | FixedPoint | Standalone |
-| CollatzBraid | FixedPoint | Standalone |
-| Various `test_native_decide` | None | Test file |
-
-**Recommendation:** These go into rs_numerics or a rs_misc catch-all.
-
---
-
-## Dependency Graph
-
-```
-rs_core (3 files, 19 sorrys)
-  └─► rs_numerics (~15 files, 0 sorrys)
-       ├─► rs_bind (~20 files)
-       │    ├─► rs_braid (~13 files)
-       │    ├─► rs_physics (~30 files)
-       │    ├─► rs_extensions (105 files)
-       │    ├─► rs_hcmmr (20 files)
-       │    ├─► rs_hardware (12 files)
-       │    ├─► rs_nii (20 files)
-       │    ├─► rs_genomic (9 files)
-       │    └─► rs_scaffold (36 files)
-       └─► rs_testing (~45 files) [leaf, not imported by others]
-```
-
---
-
-## Sorry Distribution
-
-| Module | Files | Sorry Count | Files with Sorry |
-|--------|-------|-------------|-----------------|
-| rs_core | 3 | 19 | 2 |
-| rs_numerics | ~15 | 0 | 0 |
-| rs_bind | ~20 | 0 | 0 |
-| rs_braid | ~13 | 0 | 0 |
-| rs_physics | ~30 | 1 | 1 |
-| rs_extensions | 105 | 0 | 0 |
-| rs_hcmmr | 20 | 0 | 0 |
-| rs_hardware | 12 | 0 | 0 |
-| rs_nii | 20 | 0 | 0 |
-| rs_genomic | 9 | 0 | 0 |
-| rs_testing | ~45 | 0 | 0 |
-| rs_scaffold | 36 | 1 | 1 |
-| **Total** | **~328** | **21** | **4** |
-
-**Note:** 55 sorrys are in the flat `Semantics/` directory files not yet assigned to modules. The 76 total sorry count includes files that need further classification.
-
---
-
-## Recommended Extraction Order
-
-1. **rs_numerics** first (FixedPoint is imported by 452 files — everything depends on it)
-2. **rs_core** second (BindAxioms → InformationManifold → T1_Coherence)
-3. **rs_bind** third (Bind + DynamicCanal)
-4. **rs_braid** fourth (clear cluster, easy to extract)
-5. **rs_testing** fifth (leaf module, no downstream deps)
-6. **rs_scaffold** sixth (already organized by subdirectory)
-7. Remaining modules in any order (rs_physics, rs_extensions, rs_hcmmr, rs_hardware, rs_nii, rs_genomic)
-
---
-
-## Open Questions
-
-1. **Should rs_extensions (105 files) be split further?** Bio/Ecology/Evolution/Cognitive are distinct domains.
-2. **What to do with the 513 flat Semantics/ files?** Many are standalone statements (axiom/theorem). Need per-file import analysis to assign to modules.
-3. **Should sorrys be addressed before or after extraction?** Extracting first makes the sorry boundaries visible.
-4. **The flat Semantics/ files contain ~55 sorrys** — these need classification before final module assignment.
--- a/package-lock.json
+++ b/package-lock.json
@ -6,11 +6,11 @@
    "": {
      "name": "research-stack",
      "dependencies": {
-        "@cline/sdk": "^0.0.59",
+        "@cline/sdk": "^0.0.54",
        "@modelcontextprotocol/inspector": "^0.22.0",
        "@modelcontextprotocol/sdk": "^1.29.0",
        "better-sqlite3": "^12.10.0",
-        "cline": "^3.0.39"
+        "cline": "^3.0.33"
      }
    },
    "node_modules/@ai-sdk/amazon-bedrock": {
@ -775,13 +775,13 @@
      }
    },
    "node_modules/@cline/agents": {
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+      "resolved": "https://registry.npmjs.org/@cline/agents/-/agents-0.0.54.tgz",
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      "license": "Apache-2.0",
      "dependencies": {
-        "@cline/llms": "0.0.59",
-        "@cline/shared": "0.0.59",
+        "@cline/llms": "0.0.54",
+        "@cline/shared": "0.0.54",
        "nanoid": "^5.1.7"
      },
      "engines": {
@ -789,9 +789,9 @@
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    },
    "node_modules/@cline/cli-darwin-arm64": {
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-      "resolved": "https://registry.npmjs.org/@cline/cli-darwin-arm64/-/cli-darwin-arm64-3.0.39.tgz",
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@ -804,9 +804,9 @@
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    "node_modules/@cline/cli-darwin-x64": {
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@ -819,9 +819,9 @@
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    "node_modules/@cline/cli-linux-arm64": {
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@ -834,9 +834,9 @@
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    },
    "node_modules/@cline/cli-linux-x64": {
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      "cpu": [
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@ -849,9 +849,9 @@
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    },
    "node_modules/@cline/cli-windows-arm64": {
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-      "resolved": "https://registry.npmjs.org/@cline/cli-windows-arm64/-/cli-windows-arm64-3.0.39.tgz",
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@ -864,9 +864,9 @@
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    "node_modules/@cline/cli-windows-x64": {
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-      "resolved": "https://registry.npmjs.org/@cline/cli-windows-x64/-/cli-windows-x64-3.0.39.tgz",
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+      "resolved": "https://registry.npmjs.org/@cline/cli-windows-x64/-/cli-windows-x64-3.0.33.tgz",
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      "cpu": [
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@ -879,13 +879,13 @@
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    },
    "node_modules/@cline/core": {
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-      "resolved": "https://registry.npmjs.org/@cline/core/-/core-0.0.59.tgz",
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+      "resolved": "https://registry.npmjs.org/@cline/core/-/core-0.0.54.tgz",
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      "dependencies": {
-        "@cline/agents": "0.0.59",
-        "@cline/llms": "0.0.59",
-        "@cline/shared": "0.0.59",
+        "@cline/agents": "0.0.54",
+        "@cline/llms": "0.0.54",
+        "@cline/shared": "0.0.54",
        "@modelcontextprotocol/sdk": "^1.29.0",
        "@opentelemetry/api": "^1.9.0",
        "@opentelemetry/api-logs": "^0.214.0",
@ -919,9 +919,9 @@
      }
    },
    "node_modules/@cline/llms": {
-      "version": "0.0.59",
-      "resolved": "https://registry.npmjs.org/@cline/llms/-/llms-0.0.59.tgz",
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        "@ai-sdk/anthropic": "^3.0.68",
@ -932,7 +932,7 @@
        "@ai-sdk/openai-compatible": "^2.0.38",
        "@ai-sdk/provider": "^3.0.8",
        "@aws-sdk/credential-providers": "^3.922.0",
-        "@cline/shared": "0.0.59",
+        "@cline/shared": "0.0.54",
        "@jerome-benoit/sap-ai-provider": "4.6.9",
        "@langfuse/otel": "^4.0.0",
        "@opentelemetry/api": "^1.9.0",
@ -959,21 +959,21 @@
      }
    },
    "node_modules/@cline/sdk": {
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      "license": "Apache-2.0",
      "dependencies": {
-        "@cline/core": "0.0.59"
+        "@cline/core": "0.0.54"
      },
      "engines": {
        "node": ">=22"
      }
    },
    "node_modules/@cline/shared": {
-      "version": "0.0.59",
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@ -2491,22 +2491,20 @@
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-        "@radix-ui/react-collection": "1.1.12",
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-        "@radix-ui/react-context": "1.2.0",
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        "@radix-ui/react-id": "1.1.2",
-        "@radix-ui/react-primitive": "2.1.7",
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-        "@radix-ui/react-use-layout-effect": "1.1.2"
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@ -2524,31 +2522,31 @@
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-        "@radix-ui/react-dismissable-layer": "1.1.15",
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        "@radix-ui/react-focus-guards": "1.1.4",
-        "@radix-ui/react-focus-scope": "1.1.12",
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-        "@radix-ui/react-primitive": "2.1.7",
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-        "@radix-ui/react-visually-hidden": "1.2.7",
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@ -2586,15 +2584,15 @@
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+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/@radix-ui/react-switch/-/react-switch-1.3.1.tgz",
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      "license": "MIT",
      "dependencies": {
-        "@radix-ui/primitive": "1.1.5",
+        "@radix-ui/primitive": "1.1.4",
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-        "@radix-ui/react-context": "1.2.0",
-        "@radix-ui/react-primitive": "2.1.7",
+        "@radix-ui/react-context": "1.1.4",
+        "@radix-ui/react-primitive": "2.1.6",
        "@radix-ui/react-use-controllable-state": "1.2.3",
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@ -2615,18 +2613,18 @@
      }
    },
    "node_modules/@radix-ui/react-tabs": {
-      "version": "1.1.17",
-      "resolved": "https://registry.npmjs.org/@radix-ui/react-tabs/-/react-tabs-1.1.17.tgz",
-      "integrity": "sha512-nRyXnrAVCwjeXcHbvEbLS6ndbTeKHG1RqCP4A8Gw5L4cemDzPXdD8rAmr6wet0v57R69wGvuIIsFjHSVkZiMzQ==",
+      "version": "1.1.15",
+      "resolved": "https://registry.npmjs.org/@radix-ui/react-tabs/-/react-tabs-1.1.15.tgz",
+      "integrity": "sha512-kxc9gI6/HfcU4nfMMVS3AmQK414kbU1IE6UCJmMmxjhO3cRPXOyYnmvyKD+ODt7q56nRq9l7Wovi6uaGwKgMlg==",
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      "dependencies": {
-        "@radix-ui/primitive": "1.1.5",
-        "@radix-ui/react-context": "1.2.0",
+        "@radix-ui/primitive": "1.1.4",
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        "@radix-ui/react-id": "1.1.2",
-        "@radix-ui/react-presence": "1.1.7",
-        "@radix-ui/react-primitive": "2.1.7",
-        "@radix-ui/react-roving-focus": "1.1.15",
+        "@radix-ui/react-presence": "1.1.6",
+        "@radix-ui/react-primitive": "2.1.6",
+        "@radix-ui/react-roving-focus": "1.1.13",
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@ -2645,23 +2643,23 @@
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    "node_modules/@radix-ui/react-toast": {
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-      "resolved": "https://registry.npmjs.org/@radix-ui/react-toast/-/react-toast-1.2.19.tgz",
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+      "resolved": "https://registry.npmjs.org/@radix-ui/react-toast/-/react-toast-1.2.17.tgz",
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-        "@radix-ui/primitive": "1.1.5",
-        "@radix-ui/react-collection": "1.1.12",
+        "@radix-ui/primitive": "1.1.4",
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-        "@radix-ui/react-presence": "1.1.7",
-        "@radix-ui/react-primitive": "2.1.7",
+        "@radix-ui/react-context": "1.1.4",
+        "@radix-ui/react-dismissable-layer": "1.1.13",
+        "@radix-ui/react-portal": "1.1.12",
+        "@radix-ui/react-presence": "1.1.6",
+        "@radix-ui/react-primitive": "2.1.6",
        "@radix-ui/react-use-callback-ref": "1.1.2",
        "@radix-ui/react-use-controllable-state": "1.2.3",
        "@radix-ui/react-use-layout-effect": "1.1.2",
-        "@radix-ui/react-visually-hidden": "1.2.7"
+        "@radix-ui/react-visually-hidden": "1.2.6"
      },
      "peerDependencies": {
        "@types/react": "*",
@ -2679,23 +2677,23 @@
      }
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    "node_modules/@radix-ui/react-tooltip": {
-      "version": "1.2.12",
-      "resolved": "https://registry.npmjs.org/@radix-ui/react-tooltip/-/react-tooltip-1.2.12.tgz",
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+      "version": "1.2.10",
+      "resolved": "https://registry.npmjs.org/@radix-ui/react-tooltip/-/react-tooltip-1.2.10.tgz",
+      "integrity": "sha512-NlNe8D0dWEpVfXFli90IO6X07Josx/b1iu98tDnx9Xv0HT4wLIL+m2VOheMHhK7qbp2HoTBqALEFzGyZs/levw==",
      "license": "MIT",
      "dependencies": {
-        "@radix-ui/primitive": "1.1.5",
+        "@radix-ui/primitive": "1.1.4",
        "@radix-ui/react-compose-refs": "1.1.3",
-        "@radix-ui/react-context": "1.2.0",
-        "@radix-ui/react-dismissable-layer": "1.1.15",
+        "@radix-ui/react-context": "1.1.4",
+        "@radix-ui/react-dismissable-layer": "1.1.13",
        "@radix-ui/react-id": "1.1.2",
-        "@radix-ui/react-popper": "1.3.3",
-        "@radix-ui/react-portal": "1.1.13",
-        "@radix-ui/react-presence": "1.1.7",
-        "@radix-ui/react-primitive": "2.1.7",
+        "@radix-ui/react-popper": "1.3.1",
+        "@radix-ui/react-portal": "1.1.12",
+        "@radix-ui/react-presence": "1.1.6",
+        "@radix-ui/react-primitive": "2.1.6",
        "@radix-ui/react-slot": "1.3.0",
        "@radix-ui/react-use-controllable-state": "1.2.3",
-        "@radix-ui/react-visually-hidden": "1.2.7"
+        "@radix-ui/react-visually-hidden": "1.2.6"
      },
      "peerDependencies": {
        "@types/react": "*",
@ -2764,11 +2762,14 @@
        }
      }
    },
-    "node_modules/@radix-ui/react-use-is-hydrated": {
-      "version": "0.1.1",
-      "resolved": "https://registry.npmjs.org/@radix-ui/react-use-is-hydrated/-/react-use-is-hydrated-0.1.1.tgz",
-      "integrity": "sha512-qwOiz4Tjo8CNnrOLAYUMXeZwDzXgXpvK4TKQPmWLECM9XoWvA6+0Z2/7Ag3A4ivjS4ovbLJPbskkxioFyBhr8A==",
+    "node_modules/@radix-ui/react-use-escape-keydown": {
+      "version": "1.1.2",
+      "resolved": "https://registry.npmjs.org/@radix-ui/react-use-escape-keydown/-/react-use-escape-keydown-1.1.2.tgz",
+      "integrity": "sha512-2uVLvLjgO7NZCWw01/FdqRwmA42J0BcjPMUCA+koFEOAb+zjqIP7SiFz/7zWPrKnVmSqr76Omq2ALyCuX4dhLw==",
      "license": "MIT",
+      "dependencies": {
+        "@radix-ui/react-use-callback-ref": "1.1.2"
+      },
      "peerDependencies": {
        "@types/react": "*",
        "react": "^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc"
@ -2846,12 +2847,12 @@
      }
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    "node_modules/@radix-ui/react-visually-hidden": {
-      "version": "1.2.7",
-      "resolved": "https://registry.npmjs.org/@radix-ui/react-visually-hidden/-/react-visually-hidden-1.2.7.tgz",
-      "integrity": "sha512-1wNZBggTDK3GRuuQ6nP4k2yi7a6l7I5qbMPbZcRsrGsGVead/f/d5FhEzUvqFs0bcrDLx7n1zKQ3JvLR6whaaw==",
+      "version": "1.2.6",
+      "resolved": "https://registry.npmjs.org/@radix-ui/react-visually-hidden/-/react-visually-hidden-1.2.6.tgz",
+      "integrity": "sha512-jCE0WljWifTI4niIMCll06kGpsJTAPiZVU9H4WR1N6qW7At9ystHbN7dDB+we2xH535roFHj7qKS+RGj0FMDWQ==",
      "license": "MIT",
      "dependencies": {
-        "@radix-ui/react-primitive": "2.1.7"
+        "@radix-ui/react-primitive": "2.1.6"
      },
      "peerDependencies": {
        "@types/react": "*",
@ -3674,9 +3675,9 @@
      "license": "MIT"
    },
    "node_modules/brace-expansion": {
-      "version": "1.1.16",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.16.tgz",
-      "integrity": "sha512-IDw48K2/2kRkg9LdJxurvq3lV3aBgq0REY89duEqFRthjlPdXHKMj7EnQOXVckxzgisinf3nHfrcE2FufFLXMw==",
+      "version": "1.1.15",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.15.tgz",
+      "integrity": "sha512-EwOCDEex4quD37XhqM3omwtMoJjr//isUZz1JopUNWms+4Z2ViyM/k1YIRePpoVNnQhENnxtFjLaxNHrT7xIUg==",
      "license": "MIT",
      "dependencies": {
        "balanced-match": "^1.0.0",
@ -3813,28 +3814,28 @@
      }
    },
    "node_modules/cline": {
-      "version": "3.0.39",
-      "resolved": "https://registry.npmjs.org/cline/-/cline-3.0.39.tgz",
-      "integrity": "sha512-T6xNCa+N9u8JV9MaA+ds4WfjnaqXCyS3qFvj1y+6dL2RV8horGbQdjWosv+KvoYO4PtQjhWVKdjKWJe2LRN1zw==",
+      "version": "3.0.33",
+      "resolved": "https://registry.npmjs.org/cline/-/cline-3.0.33.tgz",
+      "integrity": "sha512-cITY6BXp4qkSAKr6tsTbSj6tF3ck9t3YG4sgYadaa0X7rMSDBja6YT90mGHb7F6kZn8OEUcGvfkorrEbJU4GPw==",
      "hasInstallScript": true,
      "license": "Apache-2.0",
      "dependencies": {
-        "@cline/agents": "0.0.59",
-        "@cline/core": "0.0.59",
-        "@cline/llms": "0.0.59",
-        "@cline/sdk": "0.0.59",
-        "@cline/shared": "0.0.59"
+        "@cline/agents": "0.0.54",
+        "@cline/core": "0.0.54",
+        "@cline/llms": "0.0.54",
+        "@cline/sdk": "0.0.54",
+        "@cline/shared": "0.0.54"
      },
      "bin": {
        "cline": "bin/cline"
      },
      "optionalDependencies": {
-        "@cline/cli-darwin-arm64": "3.0.39",
-        "@cline/cli-darwin-x64": "3.0.39",
-        "@cline/cli-linux-arm64": "3.0.39",
-        "@cline/cli-linux-x64": "3.0.39",
-        "@cline/cli-windows-arm64": "3.0.39",
-        "@cline/cli-windows-x64": "3.0.39"
+        "@cline/cli-darwin-arm64": "3.0.33",
+        "@cline/cli-darwin-x64": "3.0.33",
+        "@cline/cli-linux-arm64": "3.0.33",
+        "@cline/cli-linux-x64": "3.0.33",
+        "@cline/cli-windows-arm64": "3.0.33",
+        "@cline/cli-windows-x64": "3.0.33"
      }
    },
    "node_modules/cliui": {
--- a/package.json
+++ b/package.json
@ -11,11 +11,11 @@
    "probe-science": "sh -c 'if [ -x .venv-science/bin/python ]; then .venv-science/bin/python scripts/probe_science_toolbelt.py; else python3 scripts/probe_science_toolbelt.py; fi'"
  },
  "dependencies": {
-    "@cline/sdk": "^0.0.59",
+    "@cline/sdk": "^0.0.54",
    "@modelcontextprotocol/inspector": "^0.22.0",
    "@modelcontextprotocol/sdk": "^1.29.0",
    "better-sqlite3": "^12.10.0",
-    "cline": "^3.0.39"
+    "cline": "^3.0.33"
  },
  "overrides": {
    "@openai/codex": "0.132.0"