diff --git a/.changeset/bootstrap-system-prompt.md b/.changeset/bootstrap-system-prompt.md
deleted file mode 100644
index 6ce341cc..00000000
--- a/.changeset/bootstrap-system-prompt.md
+++ /dev/null
@@ -1,5 +0,0 @@
----
-'@gemstack/framework': minor
----
-
-Add bootstrap mode (`--bootstrap`, and `StartRunOptions.bootstrap` for the dashboard): starting a brand-new project from an empty directory. It prepends a forceful preamble above the built-in #326 prompt so the first turn stops for a plan (ranked interpretations or a PLAN file) instead of charging ahead and scaffolding code. The #326 template is left byte-identical; the preamble only raises its "Unclear scope" / "Large scope" rules above Claude Code's default decisiveness, which otherwise overrides them on the append path (#297, #448).
diff --git a/packages/framework/src/cli.test.ts b/packages/framework/src/cli.test.ts
index 7bda070c..9ad037b2 100644
--- a/packages/framework/src/cli.test.ts
+++ b/packages/framework/src/cli.test.ts
@@ -61,11 +61,6 @@ test('parseArgs collects repeatable --context directories (#439)', () => {
   assert.deepEqual(parseArgs(['--context', '/work/api', '--context', '/work/ui', 'x']).context, ['/work/api', '/work/ui'])
 })
 
-test('parseArgs reads --bootstrap (#297/#448)', () => {
-  assert.equal(parseArgs(['x']).bootstrap, false)
-  assert.equal(parseArgs(['--bootstrap', 'x']).bootstrap, true)
-})
-
 test('parseArgs reads --post-merge (#326)', () => {
   assert.equal(parseArgs(['x']).postMerge, false)
   assert.equal(parseArgs(['--post-merge', 'x']).postMerge, true)
diff --git a/packages/framework/src/cli.ts b/packages/framework/src/cli.ts
index fab882f7..c6579766 100644
--- a/packages/framework/src/cli.ts
+++ b/packages/framework/src/cli.ts
@@ -152,9 +152,6 @@ Options:
   --context <dir>        Focus the agent on this directory (repeatable). Adds one
                          "Context: <dirs>" line to the system prompt; the agent can
                          still reach every repo, this just narrows where it looks.
-  --bootstrap            Bootstrap mode: a brand-new project from an empty dir. Makes
-                         the first turn stop for a plan (interpretations / PLAN) before
-                         writing any code, instead of charging ahead.
   --post-merge           When the run signals setReadyForMerge(), fire the post-merge
                          quality suite: maintainability, readability, and security-audit
                          prompts, one after another (#326).
@@ -230,8 +227,6 @@ export interface CliOptions {
   eco: Required<EcoOptions>
   /** `--context <dir>` (repeatable): in-context directories added as one `Context:` line (#439). */
   context: string[]
-  /** `--bootstrap`: bootstrap mode (#297/#448) — a new project from an empty dir; stop for a plan first. */
-  bootstrap: boolean
   /** `--post-merge`: fire the #326 post-merge quality suite (maintainability/readability/security-audit) when the run signals setReadyForMerge(). */
   postMerge: boolean
   /** `--browser`: give the agent a real browser via chrome-devtools-mcp (navigate, console, network, DOM, screenshot) during the run (#452). */
@@ -295,7 +290,6 @@ export function parseArgs(argv: string[]): CliOptions {
     vanilla: false,
     eco: { autoPlanning: false, autoResearch: false, autoMaintenance: false },
     context: [],
-    bootstrap: false,
     postMerge: false,
     browser: false,
     dashboard: true,
@@ -343,9 +337,6 @@ export function parseArgs(argv: string[]): CliOptions {
       case '--vanilla':
         opts.vanilla = true
         break
-      case '--bootstrap':
-        opts.bootstrap = true
-        break
       case '--post-merge':
         opts.postMerge = true
         break
@@ -1009,7 +1000,6 @@ export async function runCli(argv: string[], io: CliIO = defaultIO): Promise<num
     if (noBuiltinPrompt) io.out(`◆ built-in system prompt: off (${opts.vanilla ? 'vanilla' : 'the-framework.yml'})`)
     else if (eco) io.out(`◆ eco: dropping ${Object.keys(eco).filter(k => eco[k as keyof EcoOptions]).join(', ')}`)
     if (opts.context.length) io.out(`◆ context: ${opts.context.join(', ')}`)
-  if (opts.bootstrap) io.out('◆ bootstrap: on (plan before building)')
     try {
       await runPrompt({
         prompt: opts.directPrompt ? intent : renderResearchPrompt(intent),
@@ -1030,7 +1020,6 @@ export async function runCli(argv: string[], io: CliIO = defaultIO): Promise<num
         ...(noBuiltinPrompt ? { antiLazyPill: false } : {}),
         ...(eco ? { eco } : {}),
         ...(opts.context.length ? { context: opts.context } : {}),
-        ...(opts.bootstrap ? { bootstrap: true } : {}),
         ...(modeList.includes('autopilot') ? { autopilot: true } : {}),
         ...((): { sessionLink?: string } => {
           const link = chooseSessionLink(opts, fake)
@@ -1118,7 +1107,6 @@ export async function runCli(argv: string[], io: CliIO = defaultIO): Promise<num
   if (noBuiltinPrompt) io.out(`◆ built-in system prompt: off (${opts.vanilla ? 'vanilla' : 'the-framework.yml'})`)
   else if (eco) io.out(`◆ eco: dropping ${Object.keys(eco).filter(k => eco[k as keyof EcoOptions]).join(', ')}`)
   if (opts.context.length) io.out(`◆ context: ${opts.context.join(', ')}`)
-  if (opts.bootstrap) io.out('◆ bootstrap: on (plan before building)')
 
   const runOpts: RunFrameworkOptions = {
     intent,
@@ -1156,7 +1144,6 @@ export async function runCli(argv: string[], io: CliIO = defaultIO): Promise<num
     ...(noBuiltinPrompt ? { antiLazyPill: false } : {}),
     ...(eco ? { eco } : {}),
     ...(opts.context.length ? { context: opts.context } : {}),
-    ...(opts.bootstrap ? { bootstrap: true } : {}),
     ...((): { sessionLink?: string } => {
       const link = chooseSessionLink(opts, fake)
       return link ? { sessionLink: link } : {}
diff --git a/packages/framework/src/client.ts b/packages/framework/src/client.ts
index 0de6f4f9..791dc862 100644
--- a/packages/framework/src/client.ts
+++ b/packages/framework/src/client.ts
@@ -25,7 +25,6 @@ export {
   composeRunSystem,
   renderSystemPrompt,
   SYSTEM_PROMPT_TEMPLATE,
-  BOOTSTRAP_PREAMBLE,
   type SystemPromptOptions,
   type RunSystemOptions,
   type TfContext,
diff --git a/packages/framework/src/daemon.test.ts b/packages/framework/src/daemon.test.ts
index 8f0e6b88..7f098b46 100644
--- a/packages/framework/src/daemon.test.ts
+++ b/packages/framework/src/daemon.test.ts
@@ -56,8 +56,6 @@ test('startOptionFlags maps only enabled Global options to CLI flags (#314)', ()
     '--context',
     '/work/ui',
   ])
-  // Bootstrap mode (#297/#448): maps to --bootstrap.
-  assert.deepEqual(startOptionFlags({ bootstrap: true }), ['--bootstrap'])
   // Post-merge quality suite (#326): maps to --post-merge.
   assert.deepEqual(startOptionFlags({ postMerge: true }), ['--post-merge'])
   // Browser via chrome-devtools-mcp (#452): maps to --browser.
diff --git a/packages/framework/src/daemon.ts b/packages/framework/src/daemon.ts
index 451b9c8d..c647dcf1 100644
--- a/packages/framework/src/daemon.ts
+++ b/packages/framework/src/daemon.ts
@@ -68,7 +68,6 @@ export function startOptionFlags(options: StartRunOptions): string[] {
   if (options.eco?.autoResearch) flags.push('--eco-auto-research')
   if (options.eco?.autoMaintenance) flags.push('--eco-auto-maintenance')
   for (const dir of options.context ?? []) if (typeof dir === 'string' && dir.trim()) flags.push('--context', dir)
-  if (options.bootstrap) flags.push('--bootstrap')
   if (options.postMerge) flags.push('--post-merge')
   if (options.browser) flags.push('--browser')
   return flags
diff --git a/packages/framework/src/dashboard/server.ts b/packages/framework/src/dashboard/server.ts
index 11243532..ee961437 100644
--- a/packages/framework/src/dashboard/server.ts
+++ b/packages/framework/src/dashboard/server.ts
@@ -93,8 +93,6 @@ export interface StartRunOptions {
   eco?: EcoOptions
   /** In-context directories (#439): each becomes a `--context <dir>` flag on the spawned run. */
   context?: string[]
-  /** Bootstrap mode (#297/#448): a new project from an empty dir; maps to `--bootstrap`. */
-  bootstrap?: boolean
   /** Post-merge quality suite (#326): on setReadyForMerge(), fire maintainability/readability/security-audit; maps to `--post-merge`. */
   postMerge?: boolean
   /** Give the agent a real browser via chrome-devtools-mcp during the run (#452); maps to `--browser`. */
diff --git a/packages/framework/src/index.ts b/packages/framework/src/index.ts
index 49c04a17..d089b939 100644
--- a/packages/framework/src/index.ts
+++ b/packages/framework/src/index.ts
@@ -224,7 +224,6 @@ export {
   composeRunSystem,
   renderSystemPrompt,
   SYSTEM_PROMPT_TEMPLATE,
-  BOOTSTRAP_PREAMBLE,
   type SystemPromptOptions,
   type RunSystemOptions,
   type TfContext,
diff --git a/packages/framework/src/prompt-run.ts b/packages/framework/src/prompt-run.ts
index cd0bde2d..4bcc133e 100644
--- a/packages/framework/src/prompt-run.ts
+++ b/packages/framework/src/prompt-run.ts
@@ -46,8 +46,6 @@ export interface RunPromptOptions {
   eco?: EcoOptions
   /** In-context directories (#439): added as one `Context:` line to the system prompt. */
   context?: readonly string[]
-  /** Bootstrap mode (#297/#448): prepend the forceful preamble so the first turn stops for a plan. Default false. */
-  bootstrap?: boolean
   /** Stop the run once the agent has spent this much, in USD (#322). */
   budgetUsd?: number
   /**
@@ -92,7 +90,7 @@ export async function runPrompt(opts: RunPromptOptions): Promise<RunPromptResult
     prompt: opts.prompt,
     params: { autopilot: opts.autopilot === true, ...(opts.eco ? { eco: opts.eco } : {}) },
   }
-  const system = composeRunSystem({ antiLazyPill: opts.antiLazyPill, user: opts.systemPrompt, tf, context: opts.context, bootstrap: opts.bootstrap })
+  const system = composeRunSystem({ antiLazyPill: opts.antiLazyPill, user: opts.systemPrompt, tf, context: opts.context })
   // The template's `# User prompt` half carries the prompt (today it renders to
   // exactly `opts.prompt`; any framing Rom adds around the slot rides along). With
   // the built-in prompt off, the raw prompt is sent as-is.
diff --git a/packages/framework/src/run.ts b/packages/framework/src/run.ts
index cadef1b6..07c7b347 100644
--- a/packages/framework/src/run.ts
+++ b/packages/framework/src/run.ts
@@ -105,11 +105,6 @@ export interface RunFrameworkOptions {
   eco?: EcoOptions
   /** In-context directories (#439): added as one `Context:` line to the system prompt. */
   context?: readonly string[]
-  /**
-   * Bootstrap mode (#297/#448): a brand-new project from an empty directory. Prepends a
-   * forceful preamble so the first turn stops for a plan instead of charging ahead. Default off.
-   */
-  bootstrap?: boolean
   /**
    * A user-picked Open Loop domain preset ({loops, prompts}) to run the build
    * under (#251). Its loops + prompts are materialized into a driver-backed {@link LoopEngine}
@@ -292,7 +287,6 @@ export async function runFramework(opts: RunFrameworkOptions): Promise<RunFramew
     user: opts.systemPrompt,
     tf,
     context: opts.context,
-    bootstrap: opts.bootstrap,
   })
 
   // The session id is not known until the first driver turn returns, so a
diff --git a/packages/framework/src/system-prompt.test.ts b/packages/framework/src/system-prompt.test.ts
index 224e4e2a..38fc05f6 100644
--- a/packages/framework/src/system-prompt.test.ts
+++ b/packages/framework/src/system-prompt.test.ts
@@ -4,7 +4,6 @@ import { mkdtemp, writeFile, rm } from 'node:fs/promises'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
 import {
-  BOOTSTRAP_PREAMBLE,
   composeRunSystem,
   renderSystemPrompt,
   systemPromptBlock,
@@ -90,6 +89,14 @@ test('systemPromptBlock prepends a Context line for the selected directories (#4
   assert.equal(systemPromptBlock({ antiLazyPill: false, user: 'x', context: ['  '] }), 'x') // blank entries dropped
 })
 
+test('systemPromptBlock is the #326 prompt and the user prompt, in that order, and nothing else (#457)', () => {
+  // The bootstrap preamble was the last text here that was neither the #326 doc nor the
+  // user's own. Measured on four live runs: #326 alone already stops an empty-dir build
+  // for a plan, so the override earned nothing and outranked the doc.
+  const block = systemPromptBlock({ user: 'Ship small PRs.', context: ['/work/api'] })
+  assert.equal(block, ['Context: /work/api', renderSystemPrompt().system, 'Ship small PRs.'].join('\n\n'))
+})
+
 test('systemPromptBlock ignores a whitespace-only user prompt', () => {
   assert.equal(systemPromptBlock({ user: '   ' }), renderSystemPrompt().system)
   assert.equal(systemPromptBlock({ antiLazyPill: false, user: '  \n ' }), '')
@@ -100,21 +107,6 @@ test('systemPromptBlock threads tf through to the template', () => {
   assert.ok(block.includes('postpone a deep refactor'))
 })
 
-test('systemPromptBlock prepends the bootstrap preamble above the built-in prompt (#297/#448)', () => {
-  const off = systemPromptBlock()
-  assert.ok(!off.includes(BOOTSTRAP_PREAMBLE)) // default off: no preamble
-  const on = systemPromptBlock({ bootstrap: true })
-  assert.ok(on.startsWith(BOOTSTRAP_PREAMBLE)) // preamble first
-  assert.ok(on.includes('# System prompt')) // then the byte-identical #326 template
-  assert.ok(on.indexOf(BOOTSTRAP_PREAMBLE) < on.indexOf('# System prompt')) // preamble outranks it
-})
-
-test('systemPromptBlock keeps the bootstrap preamble after the Context line (#439/#448)', () => {
-  const block = systemPromptBlock({ bootstrap: true, context: ['/work/api'] })
-  assert.ok(block.startsWith('Context: /work/api')) // context frames everything
-  assert.ok(block.indexOf('Context: /work/api') < block.indexOf(BOOTSTRAP_PREAMBLE))
-})
-
 test('eco.autoPlanning drops only the Large scope section (#314)', () => {
   const { system } = renderSystemPrompt({ prompt: 'x', params: { eco: { autoPlanning: true } } })
   assert.ok(!system.includes('## Large scope'))
@@ -180,13 +172,11 @@ test('composeRunSystem appends nothing after the protocols, whatever the options
   const system = composeRunSystem({
     user: 'Ship small PRs.',
     context: ['/work/api'],
-    bootstrap: true,
     tf: { prompt: 'build a todo app', params: { autopilot: true } },
   })
   const block = systemPromptBlock({
     user: 'Ship small PRs.',
     context: ['/work/api'],
-    bootstrap: true,
     tf: { prompt: 'build a todo app', params: { autopilot: true } },
   })
   assert.equal(system, [block, AWAIT_PROTOCOL, SIGNAL_PROTOCOL].join('\n\n'))
diff --git a/packages/framework/src/system-prompt.ts b/packages/framework/src/system-prompt.ts
index c9429f34..5bb8205a 100644
--- a/packages/framework/src/system-prompt.ts
+++ b/packages/framework/src/system-prompt.ts
@@ -63,22 +63,6 @@ Before starting to write code, measure "variability":
 
 \${{tf.prompt}}`
 
-/**
- * Bootstrap mode's forceful preamble (#297/#448). The built-in #326 prompt already
- * carries the "Unclear scope" / "Large scope" rules, but appended to Claude Code's own
- * system prompt those lose to its default "be decisive, don't block the user" instinct —
- * so a fresh-from-empty-dir build charges ahead instead of stopping for a plan (measured).
- * This preamble states the override explicitly and forbids writing code before approval,
- * which flips the behaviour without touching Rom's template. Prepended above the #326
- * prompt only when bootstrap mode is on.
- */
-export const BOOTSTRAP_PREAMBLE = `# Bootstrap mode
-
-You are starting a brand-new project from an empty directory. This takes precedence over any default tendency to act decisively or to start building right away:
-
-- Do NOT write, scaffold, or edit any file, and do NOT run build or install commands, until the user has approved a plan.
-- Your first reply MUST be either a list of interpretations sorted by plausibility (when the scope is unclear) or a plan the user can approve (when the scope is large), then stop and await the user's answer.`
-
 /**
  * Eco fine-grained control (#314): each flag drops one whole `##` section from the
  * built-in #326 prompt to save tokens, letting the agent auto-handle that concern.
@@ -187,12 +171,6 @@ export interface SystemPromptOptions {
    * the block. Empty/absent adds nothing.
    */
   context?: readonly string[] | undefined
-  /**
-   * Bootstrap mode (#297/#448): starting a brand-new project from an empty directory.
-   * Prepends the forceful {@link BOOTSTRAP_PREAMBLE} above the built-in prompt so the
-   * first turn stops for a plan instead of charging ahead. Default off.
-   */
-  bootstrap?: boolean | undefined
 }
 
 /**
@@ -209,9 +187,6 @@ export function systemPromptBlock(opts: SystemPromptOptions = {}): string {
   // alone under `--vanilla`, where there is no built-in prompt to frame).
   const context = opts.context?.map(d => d.trim()).filter(Boolean)
   if (context && context.length) parts.push(`Context: ${context.join(', ')}`)
-  // Bootstrap's override sits above the #326 prompt so it frames (and outranks) its
-  // "Unclear scope" / "Large scope" rules.
-  if (opts.bootstrap) parts.push(BOOTSTRAP_PREAMBLE)
   if (opts.antiLazyPill !== false) parts.push(renderSystemPrompt(opts.tf).system)
   const user = opts.user?.trim()
   if (user) parts.push(user)
@@ -228,8 +203,8 @@ export type RunSystemOptions = SystemPromptOptions
  * builds (#500): the two sites each inlined the composition and one nested the protocols
  * inside the built-in-prompt branch.
  *
- * Order is fixed: the #326 prompt block (context / bootstrap / built-in prompt / user
- * SYSTEM.md) first, then the always-on emit protocols. Nothing else is appended — a
+ * Order is fixed: the #326 prompt block (context / built-in prompt / user SYSTEM.md)
+ * first, then the always-on emit protocols. Nothing else is appended — a
  * build run's system channel is exactly this (#547), which is what lets the dashboard
  * show the whole prompt before a run starts (#520). The protocols are unconditional —
  * they are the *emit contract* (how the agent signals an awaited choice and the