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/llm/llm-deepseek/tests/adapter.e2e.ts

@@ -0,0 +1,148 @@
+import { afterEach, describe, expect, it } from 'vitest'
+import { Context } from 'cordis'
+import LlmService, { CallId } from '@deepseek-ai/dsh-llm'
+import type { GenerateResult, Message, ToolSchema } from '@deepseek-ai/dsh-llm'
+import * as LlmDeepSeek from '@deepseek-ai/dsh-llm-deepseek'
+import type { Config } from '@deepseek-ai/dsh-llm-deepseek'
+
+/**
+ * Real-API e2e for the hand-rolled adapter: V4 Flash + V4 Pro across
+ * thinking modes and both official effort levels. Key-gated — skips
+ * entirely without $DEEPSEEK_API_KEY (see vitest.e2e.config.ts).
+ */
+
+const FLASH = 'deepseek-v4-flash'
+const PRO = 'deepseek-v4-pro'
+const contexts: Context[] = []
+
+async function harness(model: string, config: Partial<Config> = {}) {
+  const ctx = new Context()
+  contexts.push(ctx)
+  await ctx.plugin(LlmService)
+  await ctx.plugin(LlmDeepSeek, { models: [model], ...config })
+  return ctx
+}
+
+afterEach(async () => {
+  await Promise.all(contexts.splice(0).map(ctx => ctx.fiber.dispose()))
+})
+
+function ask(text: string): Message[] {
+  return [{ role: 'user', content: [{ type: 'text', text }] }]
+}
+
+function textOf(result: GenerateResult): string {
+  return result.message.content
+    .filter(block => block.type === 'text')
+    .map(block => block.text)
+    .join('')
+}
+
+const weatherTool: ToolSchema = {
+  name: 'get_weather',
+  description: 'Get the current weather for a city.',
+  parameters: {
+    type: 'object',
+    properties: { city: { type: 'string', description: 'City name' } },
+    required: ['city'],
+  },
+}
+
+describe.skipIf(!process.env.DEEPSEEK_API_KEY)('llm-deepseek e2e (real API)', () => {
+  it('flash + thinking disabled: plain text generation', async () => {
+    const ctx = await harness(FLASH, { thinking: 'disabled' })
+    const result = await ctx.llm.generate({
+      model: FLASH,
+      messages: ask('Reply with exactly the word: pong'),
+      maxTokens: 50,
+    })
+    expect(result.finish.kind).toBe('stop')
+    expect(textOf(result).toLowerCase()).toContain('pong')
+    expect(result.message.content.some(block => block.type === 'reasoning')).toBe(false)
+    expect(result.usage?.inputTokens).toBeGreaterThan(0)
+    expect(result.usage?.outputTokens).toBeGreaterThan(0)
+  })
+
+  it('flash + thinking enabled (effort high): reasoning blocks + reasoning tokens', async () => {
+    const ctx = await harness(FLASH, { thinking: 'enabled', reasoningEffort: 'high' })
+    const result = await ctx.llm.generate({
+      model: FLASH,
+      messages: ask('Which is larger, 9.11 or 9.8? Answer with just the number.'),
+      maxTokens: 2000,
+    })
+    expect(result.finish.kind).toBe('stop')
+    expect(result.message.content.some(block => block.type === 'reasoning')).toBe(true)
+    expect(textOf(result)).toContain('9.8')
+    expect(result.usage?.reasoningTokens).toBeGreaterThan(0)
+  })
+
+  it.each(['high', 'max'] as const)(
+    'pro + thinking enabled (effort %s): tool-call round trip with reasoning passback',
+    async (effort) => {
+      const ctx = await harness(PRO, { thinking: 'enabled', reasoningEffort: effort })
+
+      // Turn 1: the model must call the tool (and think before it).
+      const first = await ctx.llm.generate({
+        model: PRO,
+        messages: ask('What is the weather in Paris right now? Use the get_weather tool.'),
+        tools: [weatherTool],
+        maxTokens: 2000,
+      })
+      expect(first.finish.kind).toBe('tool-calls')
+      const call = first.message.content.find(block => block.type === 'tool-call')
+      expect(call).toBeDefined()
+      expect(call!.name).toBe('get_weather')
+      expect(JSON.parse(call!.arguments)).toMatchObject({ city: expect.stringMatching(/paris/i) as string })
+
+      // Turn 2: send the tool result back WITH the assistant's reasoning
+      // block in history (the official thinking+tools passback rule).
+      const second = await ctx.llm.generate({
+        model: PRO,
+        messages: [
+          ...ask('What is the weather in Paris right now? Use the get_weather tool.'),
+          { role: 'assistant', content: first.message.content },
+          {
+            role: 'user',
+            content: [{
+              type: 'tool-result',
+              toolCallId: CallId(call!.id),
+              content: [{ type: 'text', text: 'Sunny, 22°C' }],
+            }],
+          },
+        ],
+        tools: [weatherTool],
+        maxTokens: 2000,
+      })
+      expect(second.finish.kind).toBe('stop')
+      expect(textOf(second).toLowerCase()).toMatch(/sunny|22/)
+    },
+  )
+
+  it('pro + thinking disabled: plain generation without reasoning blocks', async () => {
+    const ctx = await harness(PRO, { thinking: 'disabled' })
+    const result = await ctx.llm.generate({
+      model: PRO,
+      messages: ask('Reply with exactly the word: pong'),
+      maxTokens: 50,
+    })
+    expect(result.finish.kind).toBe('stop')
+    expect(result.message.content.some(block => block.type === 'reasoning')).toBe(false)
+  })
+
+  it('streams raw chunks in protocol order', async () => {
+    const ctx = await harness(FLASH, { thinking: 'disabled' })
+    const kinds: string[] = []
+    for await (const chunk of ctx.llm.stream({
+      model: FLASH,
+      messages: ask('Count from 1 to 5, digits only.'),
+      maxTokens: 50,
+    })) {
+      kinds.push(chunk.type)
+    }
+    expect(kinds[0]).toBe('block-start')
+    expect(kinds.at(-1)).toBe('finish')
+    expect(kinds.filter(kind => kind === 'finish')).toHaveLength(1)
+    // usage precedes finish (deferred-emit contract)
+    expect(kinds.indexOf('usage')).toBeLessThan(kinds.indexOf('finish'))
+  })
+})