fix(coding-agent): close remaining extension-flag edge cases (GPT-5.5 review)

Three issues from an adversarial review, all rooted in the startup argv parse
running before extensions load:

1. Flag-looking string values (`--name --print`): the extension-aware reparse
   consumed the following token as the value, disagreeing with the startup
   parse that treated `--print` as the built-in flag — so the reparse could
   silently flip command shape. Extension string flags now consume a following
   token only in `--flag=value` form or when it is not flag-looking; pass a
   flag-looking value as `--flag=value`. Keeps both parses consistent.

2. `@file` string values (`--target @notes.md`): file args were processed from
   the startup parse, which misreads the value as a file and reads it into the
   prompt. processFileArguments now runs on the extension-aware parse
   (initialArgs.fileArgs); pipedInput stays early for mode detection.

3. Built-in collisions: an extension flag named like a built-in (e.g. `model`)
   was consumed by the built-in branch and never delivered to the runner.
   registerFlag now rejects names in BUILTIN_FLAG_NAMES with a clear error
   (isolated per-extension by loadExtension's try/catch).

Adds tests for all three plus the documented startup-parse misclassification.

packages/coding-agent/src/cli/args.ts

@@ -54,6 +54,54 @@ export interface Args {
 	unknownFlags: Map<string, boolean | string>;
 }
 
+/**
+ * Long names of every built-in CLI flag recognized by {@link parseArgs}.
+ * Extension flags that would shadow one of these are rejected at registration
+ * (see ExtensionAPI.registerFlag), because a built-in branch in parseArgs would
+ * consume the flag before the extension ever sees it. Keep in sync with the
+ * flag branches below.
+ */
+export const BUILTIN_FLAG_NAMES: ReadonlySet<string> = new Set([
+	"help",
+	"version",
+	"allow-home",
+	"mode",
+	"continue",
+	"resume",
+	"session",
+	"fork",
+	"provider",
+	"model",
+	"smol",
+	"slow",
+	"plan",
+	"api-key",
+	"system-prompt",
+	"append-system-prompt",
+	"provider-session-id",
+	"no-session",
+	"session-dir",
+	"models",
+	"no-tools",
+	"no-lsp",
+	"no-pty",
+	"tools",
+	"thinking",
+	"print",
+	"export",
+	"hook",
+	"extension",
+	"plugin-dir",
+	"no-extensions",
+	"no-skills",
+	"no-rules",
+	"no-title",
+	"auto-approve",
+	"yolo",
+	"approval-mode",
+	"skills",
+	"list-models",
+]);
 export function parseArgs(inputArgs: string[], extensionFlags?: Map<string, { type: "boolean" | "string" }>): Args {
 	// Work on a copy: the `--option=value` handling below splices the value
 	// into the array, and callers reuse the same argv (the post-extension
@@ -216,7 +264,14 @@ export function parseArgs(inputArgs: string[], extensionFlags?: Map<string, { ty
 				if (extFlag.type === "boolean") {
 					result.unknownFlags.set(flagName, true);
 				} else if (extFlag.type === "string" && i + 1 < args.length) {
-					result.unknownFlags.set(flagName, args[++i]);
+					// Consume the value in `--flag=value` form, or when the next token
+					// is not flag-looking. A `-`-prefixed token in space form is left
+					// to be parsed as its own flag, so this extension-aware parse agrees
+					// with the extension-unaware startup parse on command shape; pass a
+					// flag-looking value as `--flag=value`.
+					if (equalsValueIndex !== -1 || !args[i + 1].startsWith("-")) {
+						result.unknownFlags.set(flagName, args[++i]);
+					}
 				}
 			}
 			// Unknown flags without extensionFlags are silently ignored (first pass)