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.

vitest.e2e.config.ts

@@ -24,7 +24,7 @@ export default defineConfig({
   // through the root tsconfig paths map; the native option cannot do this.
   plugins: [tsconfigPaths({ projects: ['./tsconfig.test.json'] })],
   test: {
-    include: ['packages/*/tests/**/*.e2e.ts', 'examples/*/tests/**/*.e2e.ts'],
+    include: ['packages/*/*/tests/**/*.e2e.ts', 'examples/*/tests/**/*.e2e.ts'],
     // Real model calls: generous timeouts, and retries for transient flakes
     // (the shared internal key hits concurrency quotas). No coverage — the
     // unit suites own the coverage gate.