diff --git a/product-surface/NODE.md b/product-surface/NODE.md
index 65a3c93..0c1cf9b 100644
--- a/product-surface/NODE.md
+++ b/product-surface/NODE.md
@@ -13,6 +13,7 @@ Relevant leaves:
 - **[interaction-modes.md](interaction-modes.md)** — How startup surface, autonomy posture, execution locality, and input targeting compose across local, headless, remote, and worker-steered sessions.
 - **[command-surface.md](command-surface.md)** — How the admitted command record set is projected differently across `/help`, `/skills`, init payloads, SDK picker metadata, and narrowed bridge-facing inventories.
 - **[startup-entrypoint-routing-and-session-handoff.md](startup-entrypoint-routing-and-session-handoff.md)** — How direct-connect URLs, `assistant`, `ssh`, and hidden handoff commands are intercepted before ordinary subcommand dispatch and routed back into the main REPL or headless runner.
+- **[root-cli-flag-contracts-and-bootstrap-overrides.md](root-cli-flag-contracts-and-bootstrap-overrides.md)** — How `-p`, stream or JSON output flags, injected settings or prompts, `--add-dir`, `--mcp-config`, `--plugin-dir`, tool and permission overrides, `--file`, and version-sensitive `--bare` rewrite startup state before the first turn.
 - **[model-and-behavior-controls.md](model-and-behavior-controls.md)** — How `/model`, `/effort`, `/fast`, `/theme`, `/color`, and `/output-style` together control runtime model choice, effort, premium speed paths, and behavior styling.
 - **[command-dispatch-and-composition.md](command-dispatch-and-composition.md)** — How the local command catalog, late dynamic skills, and session-scoped MCP overlay compose into one ordered slash surface.
 - **[prompt-command-and-skill-execution.md](prompt-command-and-skill-execution.md)** — How prompt-backed slash commands and SkillTool calls divide inline query re-entry, worker-backed fork execution, coordinator summaries, and turn-scoped permission or model overrides.
diff --git a/product-surface/root-cli-flag-contracts-and-bootstrap-overrides.md b/product-surface/root-cli-flag-contracts-and-bootstrap-overrides.md
new file mode 100644
index 0000000..7f266c0
--- /dev/null
+++ b/product-surface/root-cli-flag-contracts-and-bootstrap-overrides.md
@@ -0,0 +1,171 @@
+---
+title: "Root CLI Flag Contracts and Bootstrap Overrides"
+owners: []
+soft_links:
+  - /product-surface/interaction-modes.md
+  - /product-surface/startup-entrypoint-routing-and-session-handoff.md
+  - /runtime-orchestration/sessions/resume-path.md
+  - /integrations/clients/structured-io-and-headless-session-loop.md
+  - /tools-and-permissions/permissions/permission-mode-transitions-and-gates.md
+  - /integrations/mcp/config-layering-policy-and-dedup.md
+  - /integrations/plugins/plugin-source-precedence-and-cache-loading.md
+  - /integrations/plugins/skill-loading-contract.md
+  - /platform-services/interactive-startup-and-project-activation.md
+  - /runtime-orchestration/turn-flow/turn-attachments-and-sidechannels.md
+  - /reconstruction-guardrails/verification-and-native-test-oracles/released-cli-e2e-test-set.md
+---
+
+# Root CLI Flag Contracts and Bootstrap Overrides
+
+The top-level `claude` entrypoint is not just a prompt-or-subcommand switch. Public root flags can change whether the runtime starts a REPL or a headless session, which settings and integrations are even loaded, what tools or prompts the first turn sees, how continuation is validated, and whether startup-local files must exist before the UI renders.
+
+A faithful rebuild needs those launch-time overrides as one explicit contract. If they are modeled only as scattered option handlers, the rewrite will accept familiar flags while quietly booting the wrong session shape.
+
+## Scope boundary
+
+This leaf covers:
+
+- public root flags on `claude` that materially reshape session startup before the first ordinary turn
+- headless-only output and streaming gates
+- launch-time injection of prompts, settings, extra directories, MCP config, plugins, agents, tools, and permission posture
+- continuation, naming, and deterministic session-ID validation at process start
+- startup file-resource downloads triggered by the public `--file` flag
+- the version-sensitive minimal or hermetic `--bare` posture exposed by the analyzed source snapshot
+
+It intentionally does not re-document:
+
+- the deeper structured transport protocol already captured in [../integrations/clients/structured-io-and-headless-session-loop.md](../integrations/clients/structured-io-and-headless-session-loop.md)
+- the full resume restoration internals already captured in [../runtime-orchestration/sessions/resume-path.md](../runtime-orchestration/sessions/resume-path.md)
+- the full MCP, plugin, skill, or permission engines beyond how root flags shape them at launch
+- hidden debug, analytics, or internal-only flags unless they affect a visible compatibility rule
+
+## Root flags mutate canonical startup state, not side channels
+
+Equivalent behavior should preserve:
+
+- root flags being interpreted before the normal session loop or local slash-command handling begins
+- early validation failures staying fail-closed and user-visible instead of accepting an incompatible flag set and silently degrading later
+- flag effects writing into the same canonical startup state used by the rest of the product, not into one-off alternate code paths that drift from ordinary runtime behavior
+- launch-time flag shaping being visible to the real live session that follows, including the command catalog, tool pool, settings view, and session metadata seen by later surfaces
+
+The clean-room point is that "accepted by commander" is not enough. A rebuild must preserve which startup flags truly change the launched session and which combinations are refused.
+
+## Headless and structured-output flags are one launch family
+
+Equivalent behavior should preserve:
+
+- `-p/--print` switching the root entrypoint into a headless or non-interactive session loop instead of the normal REPL
+- `--output-format` only mattering on that headless path, with distinct text, JSON-envelope, and stream-JSON outcomes
+- `--input-format stream-json` requiring the structured headless path instead of being accepted in the interactive REPL
+- stream-JSON output remaining gated by the observed packaging rules, including the visible compatibility checks around verbose or streaming posture
+- `--include-partial-messages` and `--replay-user-messages` being stream-oriented launch modifiers, not generic flags that do anything useful on ordinary text output
+- `--json-schema` enabling a dedicated structured machine-output channel instead of pretending the human-readable `result` field itself becomes schema-stable
+- `--no-session-persistence` being headless-only and severing ordinary later continuation semantics for that invocation
+- budget- or fallback-style flags such as `--max-budget-usd` and `--fallback-model` behaving like headless launch posture controls rather than ordinary long-lived settings mutations
+
+The important reconstruction rule is that print-mode flags are not just formatting sugar. They switch the product onto a different session surface with narrower compatibility rules.
+
+## Continuation, identity, and naming are validated before the session boots
+
+Equivalent behavior should preserve:
+
+- `--continue` and `--resume` remaining continuation requests, not aliases for a fresh session with copied transcript text
+- explicit `--session-id` validation happening before local startup continues, including early rejection of malformed local UUIDs
+- local fresh-session IDs being rejected when they would collide with an already existing session identity
+- `--session-id` staying restricted when it is paired with `--continue` or `--resume`, so fresh IDs do not silently overwrite an existing continuation path unless a fork-style branch of behavior was explicitly requested
+- remote or tagged session-ID modes being allowed to bypass local UUID-only assumptions when the session authority is no longer purely local
+- `-n/--name` acting as a startup display-name override that affects the live session identity surface, including resume-facing labels and terminal-title style affordances, without creating orphaned session artifacts before the real session exists
+
+The product requirement is that these flags shape session identity before the first turn, not after the runtime already committed to another session lineage.
+
+## Launch-time bootstrap injection is explicit and source-aware
+
+Equivalent behavior should preserve:
+
+- `--settings` being able to inject either a path-backed settings layer or an inline JSON layer at launch
+- `--setting-sources` being parsed early enough that later settings loading, plugin state, and other source-aware bootstrap steps actually honor the narrowed source set
+- `--system-prompt` and `--append-system-prompt` feeding the canonical system-prompt builder used by real turns rather than a separate prompt wrapper
+- mutually exclusive prompt-source variants failing closed when incompatible prompt flags are supplied together
+- `--add-dir` expanding more than simple filesystem reach: it also contributes explicit extra discovery roots for instruction or skill surfaces that are allowed to honor explicit external directories
+- `--mcp-config` accepting both file-backed and inline JSON MCP definitions as explicit launch-time injection
+- `--strict-mcp-config` narrowing the live MCP surface to only the explicitly supplied MCP config instead of merely adding extra servers on top of all other discovery sources
+- `--plugin-dir` acting as session-only plugin injection that changes the live command, hook, MCP, agent, or LSP surface for that process only
+- session-only plugin injection still remaining subordinate to higher-precedence administrative or managed restrictions instead of becoming a bypass path
+- `--agents` injecting session-scoped custom agent definitions while `--agent` selects the active agent for the launched session
+- `--tools`, `--allowedTools`, and `--disallowedTools` shaping the real initial tool surface, not merely decorating the prompt or only affecting one later sub-flow
+- `--permission-mode` entering through the same centralized permission-mode transition model used by interactive changes later in the session
+- `--allow-dangerously-skip-permissions` acting as an explicit launch-time opt-in that makes a full bypass posture legally available without necessarily forcing the session to start there immediately
+- `--dangerously-skip-permissions` acting as a stronger launch request that still must survive the product's startup safety gates instead of bypassing them blindly
+- later attempts to enter `bypassPermissions` remaining invalid when the session was not launched with the required dangerous-bypass opt-in posture
+- startup toggles such as `--ide`, `--chrome`, and `--no-chrome` remaining launch-time integration posture controls rather than synthetic transcript commands
+
+The reconstruction-critical point is that these flags do not all have the same precedence or persistence, but they do all belong to one startup override family.
+
+## Explicit launch inputs stay explicit even when discovery is narrowed
+
+Equivalent behavior should preserve:
+
+- explicit launch-time injections continuing to matter even when automatic discovery is otherwise narrowed
+- source filters, plugin locks, and policy gates still being allowed to refuse some explicit inputs when the product's security or governance contract requires it
+- explicit additions such as `--add-dir`, `--plugin-dir`, `--agents`, or `--mcp-config` not being quietly dropped just because ordinary auto-discovery was reduced
+- discovery narrowing and policy narrowing staying distinct concepts: one changes what the product auto-loads, while the other can still block explicit user intent
+
+This distinction is load-bearing because the observed product treats "skip what I did not ask for" differently from "pretend what I asked for never existed."
+
+## `--bare` is a version-sensitive minimal posture, not an imaginary flag
+
+The analyzed source snapshot exposes a public or minimally public `--bare` launch mode that is not advertised in the local `claude 2.1.19` help surface on this machine. A faithful rebuild should therefore treat bare mode as **version-sensitive and evidence-backed**, not as a universal guarantee and not as an invented internal-only rumor.
+
+Equivalent behavior should preserve:
+
+- bare mode acting as one-switch minimal or hermetic startup posture rather than as a random pile of small feature disables
+- bare mode suppressing broad classes of automatic bootstrap work such as hook execution, automatic discovery, background prefetch, plugin sync, LSP startup, auto-memory, keychain or OAuth convenience reads, and similar non-essential startup layers
+- bare mode still honoring explicit launch-time inputs such as injected prompts, explicit settings, extra directories, explicit MCP config, injected agents, or session-only plugins when those inputs are otherwise allowed
+- bare mode narrowing first-party auth posture toward explicit API-key-style or similarly hermetic credentials instead of silently falling back to keychain or browser-backed OAuth discovery
+- bare mode not bypassing policy or managed locks; it is a narrower startup mode, not an admin override
+
+The clean-room insight is that bare mode means "skip ambient discovery and convenience," not "ignore explicit intent" and not "disable security."
+
+## `--file` seeds startup-local files before the session becomes usable
+
+Equivalent behavior should preserve:
+
+- `--file <file_id>:<relative_path>` acting as a real root-entrypoint bootstrap flag rather than a later slash-command surface
+- repeated file specs and space-expanded file-spec groups being parsed into one launch-time download list
+- malformed file specs not producing half-valid path state; invalid entries should fail or be skipped explicitly rather than silently mutating arbitrary files
+- startup file downloads requiring a session-ingress-style auth token and failing early with a clear error when that token is unavailable
+- the session identity used for file download pathing preferring the authoritative remote session identity when one exists, and otherwise using the local session identity
+- download targets being normalized into a session-scoped uploads namespace under the current workspace instead of writing arbitrary absolute destinations
+- path traversal above that workspace-scoped upload area being rejected explicitly
+- redundant incoming `uploads/` prefixes being cleaned up so callers do not accidentally create doubly nested upload directories
+- downloads being allowed to start early in startup, but the REPL or first interactive use still waiting until those files are locally available
+- bounded parallel download behavior instead of one fully serial fetch path for multi-file startup bundles
+- partial per-file failure surfacing as a visible warning summary while catastrophic download-path failures still fail the launch
+- successfully downloaded files becoming normal local artifacts for later prompt, attachment, or tool flows rather than remaining remote-only opaque handles
+
+This flag matters because it turns a remote file handle into local pre-turn state. If a rebuild omits that bridge, the same public command line will launch into a materially different working context.
+
+## Failure modes
+
+- **accepted-but-ignored flags**: the CLI parser accepts a public launch flag, but startup never mutates the real session state that later surfaces read
+- **headless compatibility leak**: stream-oriented or no-persistence flags appear to work outside the headless path and then silently degrade
+- **source-filter bypass**: `--setting-sources` or `--strict-mcp-config` is parsed, but later loaders still read suppressed sources
+- **tool-surface drift**: `--tools`, `--allowedTools`, or `--disallowedTools` changes one code path but not the actual live tool pool presented to the session
+- **bare-mode amnesia**: minimal mode suppresses automatic discovery but also wrongly discards explicit launch-time inputs the user asked for
+- **policy bypass through explicit injection**: `--plugin-dir`, `--mcp-config`, or `--add-dir` is treated as stronger than managed or policy restrictions when the observed product would still block it
+- **continuation identity clobber**: `--session-id` or `--name` is applied too late and overwrites existing continuation state incorrectly
+- **upload-path escape**: `--file` writes outside the session-scoped upload namespace or double-nests upload roots unpredictably
+- **startup file race**: the REPL renders before required downloaded files exist locally, so the first visible turn sees a different workspace than the user requested
+
+## Test Design
+
+In the observed source and local CLI evidence, this area is protected by packaged CLI acceptance behavior, headless protocol tests, and runtime comparison checks across real entrypoints.
+
+Equivalent coverage should prove:
+
+- root-entry flag parsing, incompatibility checks, and fail-closed error messages match the packaged CLI behavior
+- headless text, JSON, stream-JSON, schema-output, replay, and no-persistence paths preserve their public compatibility matrix
+- session identity, continuation, and naming flags shape startup state before the first turn and survive later resume-facing inspection correctly
+- explicit source-injection flags for settings, extra dirs, MCP, plugins, agents, tools, and permission posture actually change the launched session in the expected precedence order
+- version-sensitive `--bare` behavior is either reproduced for the targeted version or explicitly marked as unsupported for that version instead of being silently ignored
+- `--file` path normalization, auth-token requirements, partial-failure warnings, and pre-render availability are covered with deterministic fixtures rather than only live remote downloads