Reorganize packages into a modular hierarchy

Move the 18 flat packages/<name> packages into role-grouped dirs:
core/, llm/, bash/, session-persistence/, ui/, support/. Group dirs are
pure containers; each package keeps its @deepseek-ai/dsh-* name.

Collapse the per-package tsconfig paths maps (base + typecheck) into one
@deepseek-ai/dsh-* wildcard with a candidate per group, and derive the
publint list from the hierarchy. Update all depth-coupled globs/configs
(workspace, tsdown, vitest, eslint, knip, tsconfig includes/refs,
per-package tsconfigs, generators, doc-script scopes, type-equiv manifest)
and the cross-package/script relative imports in tests.

Fix doc-typecheck's workspacePaths() to parse tsconfig JSONC via the
TypeScript API instead of a regex comment-strip, which corrupted the
new wildcard `/*/` path candidates.

WIP: doc cross-links and package/RFC docs still to update.

packages/acp/tsconfig.json

@@ -1,18 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" },
-    { "path": "../../vendor/schemastery" },
-    { "path": "../llm" },
-    { "path": "../session" },
-    { "path": "../agent" },
-    { "path": "../tools" },
-    { "path": "../session-persistence" }
-  ]
-}

packages/agent-loop/tsconfig.json

@@ -1,19 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" },
-    { "path": "../../vendor/schemastery" },
-    { "path": "../llm" },
-    { "path": "../session" },
-    { "path": "../session-persistence" },
-    { "path": "../system-prompt" },
-    { "path": "../tools" },
-    { "path": "../agent" }
-  ]
-}

packages/agent/tsconfig.json

@@ -1,14 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" },
-    { "path": "../llm" },
-    { "path": "../session" }
-  ]
-}

packages/bash-local/tsconfig.json

@@ -1,14 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" },
-    { "path": "../../vendor/schemastery" },
-    { "path": "../bash" }
-  ]
-}

packages/bash/bash-local/tsconfig.json

@@ -0,0 +1,24 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../../vendor/schemastery"
+    },
+    {
+      "path": "../../bash/bash"
+    }
+  ]
+}

packages/bash/bash/tsconfig.json

@@ -0,0 +1,18 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    }
+  ]
+}

packages/bash/tool-bash/tests/integration.spec.ts

@@ -9,7 +9,7 @@ import AgentRegistry from '@deepseek-ai/dsh-agent'
 import AgentLoop, { ReactLoopAgent } from '@deepseek-ai/dsh-agent-loop'
 import { LocalBashExecutor } from '@deepseek-ai/dsh-bash-local'
 import * as ToolBash from '@deepseek-ai/dsh-tool-bash'
-import { MockAdapter, textResponse, toolCallResponse } from '../../agent-loop/tests/mock-adapter.ts'
+import { MockAdapter, textResponse, toolCallResponse } from '../../../core/agent-loop/tests/mock-adapter.ts'
 
 /**
  * Full-loop integration: a scripted mock model drives the REAL bash tool

packages/bash/tool-bash/tsconfig.json

@@ -0,0 +1,30 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../llm/llm"
+    },
+    {
+      "path": "../../core/tools"
+    },
+    {
+      "path": "../../core/agent"
+    },
+    {
+      "path": "../../bash/bash"
+    }
+  ]
+}

packages/bash/tsconfig.json

@@ -1,12 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" }
-  ]
-}

packages/core/agent-loop/tsconfig.json

@@ -0,0 +1,39 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../../vendor/schemastery"
+    },
+    {
+      "path": "../../llm/llm"
+    },
+    {
+      "path": "../../core/session"
+    },
+    {
+      "path": "../../session-persistence/session-persistence"
+    },
+    {
+      "path": "../../core/system-prompt"
+    },
+    {
+      "path": "../../core/tools"
+    },
+    {
+      "path": "../../core/agent"
+    }
+  ]
+}

packages/core/agent/tests/gen-cordis-catalog.spec.ts

@@ -14,13 +14,13 @@ import { mkdtempSync, mkdirSync, rmSync, writeFileSync } from 'node:fs'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
 import { afterEach, describe, expect, it } from 'vitest'
-import { collectEvents } from '../../../scripts/gen-cordis-catalog.ts'
+import { collectEvents } from '../../../../scripts/gen-cordis-catalog.ts'
 
 /** Write a fixture package exposing one `interface Events` block and return the
  * scan root to hand `collectEvents`. */
 function fixtureRoot(eventsBlock: string): string {
   const root = mkdtempSync(join(tmpdir(), 'cordis-catalog-'))
-  const dir = join(root, 'packages', 'fix', 'src')
+  const dir = join(root, 'packages', 'group', 'fix', 'src')
   mkdirSync(dir, { recursive: true })
   writeFileSync(
     join(dir, 'index.ts'),

packages/core/agent/tsconfig.json

@@ -0,0 +1,24 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../llm/llm"
+    },
+    {
+      "path": "../../core/session"
+    }
+  ]
+}

packages/core/session/tsconfig.json

@@ -0,0 +1,21 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../llm/llm"
+    }
+  ]
+}

packages/core/system-prompt/tsconfig.json

@@ -0,0 +1,21 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../llm/llm"
+    }
+  ]
+}

packages/core/tools/tsconfig.json

@@ -0,0 +1,27 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../llm/llm"
+    },
+    {
+      "path": "../../core/system-prompt"
+    },
+    {
+      "path": "../../core/agent"
+    }
+  ]
+}

packages/invariants/tsconfig.json

@@ -1,15 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" },
-    { "path": "../llm" },
-    { "path": "../session" },
-    { "path": "../agent" }
-  ]
-}

packages/llm-deepseek/tsconfig.json

@@ -1,14 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" },
-    { "path": "../../vendor/schemastery" },
-    { "path": "../llm" }
-  ]
-}

packages/llm-pi-ai/tsconfig.json

@@ -1,14 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" },
-    { "path": "../../vendor/schemastery" },
-    { "path": "../llm" }
-  ]
-}

packages/llm-replay/tsconfig.json

@@ -1,14 +0,0 @@
-{
-  "extends": "../../tsconfig.base.json",
-  "compilerOptions": {
-    "rootDir": "src",
-    "outDir": "lib"
-  },
-  "include": ["src"],
-  "references": [
-    { "path": "../../vendor/cosmokit" },
-    { "path": "../../vendor/cordis" },
-    { "path": "../llm" },
-    { "path": "../session" }
-  ]
-}

packages/llm/llm-deepseek/tsconfig.json

@@ -0,0 +1,24 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../../vendor/schemastery"
+    },
+    {
+      "path": "../../llm/llm"
+    }
+  ]
+}

packages/llm/llm-pi-ai/tsconfig.json

@@ -0,0 +1,24 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "compilerOptions": {
+    "rootDir": "src",
+    "outDir": "lib"
+  },
+  "include": [
+    "src"
+  ],
+  "references": [
+    {
+      "path": "../../../vendor/cosmokit"
+    },
+    {
+      "path": "../../../vendor/cordis"
+    },
+    {
+      "path": "../../../vendor/schemastery"
+    },
+    {
+      "path": "../../llm/llm"
+    }
+  ]
+}