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/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"
+    }
+  ]
+}