diff --git a/.changeset/calm-shells-guard.md b/.changeset/calm-shells-guard.md
new file mode 100644
index 00000000..982a8376
--- /dev/null
+++ b/.changeset/calm-shells-guard.md
@@ -0,0 +1,5 @@
+---
+"openwiki": patch
+---
+
+fix: restrict shell execution during repository documentation runs
diff --git a/src/agent/docs-only-backend.ts b/src/agent/docs-only-backend.ts
index 68b1a2c8..f2280767 100644
--- a/src/agent/docs-only-backend.ts
+++ b/src/agent/docs-only-backend.ts
@@ -68,6 +68,20 @@ const allowedIgnoredShellCommands = [
   /^rm\s+-f\s+(?:\.\/)?openwiki\/_plan\.md$/u,
 ];
 
+/**
+ * Read-only shell commands that remain available during repository init/update.
+ *
+ * Repository docs-only runs cannot safely admit arbitrary shell syntax: even a
+ * command that normally reads can be combined with redirection, substitution,
+ * aliases, or a second process to mutate paths outside `openwiki/`. Keep this
+ * list smaller than the `.openwikiignore` maintenance allowlist; deterministic
+ * host-side cleanup removes `_plan.md`, so the agent itself needs no shell write.
+ */
+const allowedDocsOnlyShellCommands = [
+  /^pwd$/u,
+  /^git\s+(?:--no-pager\s+)?rev-parse\s+HEAD$/u,
+];
+
 /**
  * Filesystem/shell backend that enforces OpenWiki's access boundaries for the
  * doc-generation agent.
@@ -79,8 +93,9 @@ const allowedIgnoredShellCommands = [
  *    denied with an error; discovery tools (`ls`/`glob`/`grep`) silently drop
  *    ignored entries; uploads/downloads reject ignored paths; and shell
  *    `execute` is restricted to a small allowlist while any rule is active.
- * 2. Docs-only confinement (`docsOnly`): in repository mode, writes are limited
- *    to the `openwiki/` tree via {@link isOpenWikiDocsPath}.
+ * 2. Docs-only confinement (`docsOnly`): in repository mode, filesystem writes
+ *    are limited to the `openwiki/` tree via {@link isOpenWikiDocsPath}, and
+ *    shell `execute` is limited to a read-only allowlist.
  *
  * Both are security boundaries against an agent that may be prompt-injected via
  * untrusted repository content, so path checks canonicalize before matching.
@@ -319,9 +334,10 @@ export class OpenWikiLocalShellBackend extends LocalShellBackend {
 
   /**
    * Run a shell command. While any `.openwikiignore` rule is active, only the
-   * {@link allowedIgnoredShellCommands} allowlist may run; anything else is
-   * refused (exit code 1) with guidance to use the gated filesystem tools,
-   * since arbitrary shell cannot be proven not to read an ignored path.
+   * {@link allowedIgnoredShellCommands} allowlist may run. Repository docs-only
+   * runs independently use {@link allowedDocsOnlyShellCommands}, preventing
+   * shell redirection or another mutation primitive from bypassing the path
+   * checks enforced by the structured filesystem methods.
    */
   override async execute(command: string): Promise<ExecuteResponse> {
     if (
@@ -335,6 +351,19 @@ export class OpenWikiLocalShellBackend extends LocalShellBackend {
       };
     }
 
+    if (
+      this.docsOnly &&
+      this.outputMode === "repository" &&
+      !isAllowedDocsOnlyShellCommand(command)
+    ) {
+      return {
+        exitCode: 1,
+        output:
+          "Shell execute is restricted during OpenWiki repository init/update runs. Use the filesystem tools for repository inspection and documentation writes.",
+        truncated: false,
+      };
+    }
+
     return super.execute(command);
   }
 
@@ -430,3 +459,14 @@ function isAllowedShellCommandWithIgnore(command: string): boolean {
     allowedCommand.test(trimmedCommand),
   );
 }
+
+/**
+ * Whether a shell command is on the repository docs-only read-only allowlist.
+ */
+function isAllowedDocsOnlyShellCommand(command: string): boolean {
+  const trimmedCommand = command.trim();
+
+  return allowedDocsOnlyShellCommands.some((allowedCommand) =>
+    allowedCommand.test(trimmedCommand),
+  );
+}
diff --git a/src/agent/prompt.ts b/src/agent/prompt.ts
index b58bc10a..c936c0d6 100644
--- a/src/agent/prompt.ts
+++ b/src/agent/prompt.ts
@@ -23,21 +23,22 @@ export function createSystemPrompt(
   const output = getOutputPromptConfig(outputMode);
   const languageInstructions = createLanguageInstructions(language);
   const ignoreActive = openWikiIgnore?.isActive === true;
+  const shellRestricted =
+    ignoreActive || (outputMode === "repository" && command !== "chat");
 
-  // When .openwikiignore is active the execute allowlist refuses shell-based
-  // discovery, so the prompt must steer to the file tools and the provided git
-  // summary instead of git/rg. When inactive these keep today's wording exactly,
-  // so the common no-ignore run is unchanged.
-  const gitHistoryHint = ignoreActive
+  // Restricted runs refuse shell-based discovery, so the prompt must steer to
+  // file tools and the provided git summary instead of suggesting git/rg calls
+  // that the backend will reject. Chat and local-wiki runs retain shell access.
+  const gitHistoryHint = shellRestricted
     ? "Use the provided git summary for repository history. "
     : "Use git through shell execute when it provides useful history. ";
-  const discoveryHint = ignoreActive
+  const discoveryHint = shellRestricted
     ? "- Do not call glob with **/* from the root. Use targeted ls, glob, and grep by directory and extension, skipping .git, node_modules, dist, build, cache directories, and existing generated wiki output."
     : "- Do not call glob with **/* from the root. Use targeted discovery by directory and extension. Prefer shell commands like rg --files with excludes for .git, node_modules, dist, build, cache directories, and existing generated wiki output.";
-  const gitDiscipline = ignoreActive
+  const gitDiscipline = shellRestricted
     ? `Git discipline:
-- A filtered git summary of repository history is provided in your context. Use it to explain why code exists, not just what it does, focusing on recent, high-signal changes.
-- The summary already excludes .openwikiignore paths. Do not run git or other shell commands to reconstruct history; shell discovery is unavailable while .openwikiignore is active.`
+- A git summary of repository history is provided in your context. Use it to explain why code exists, not just what it does, focusing on recent, high-signal changes.
+- Do not run git or other shell commands to reconstruct history; shell discovery is unavailable for this run.`
     : `Git discipline:
 - Use git heavily where it helps explain why code exists, not just what code exists.
 - During init, inspect recent commit history and use git log, git show, or git blame selectively on important files to understand how major workflows, entrypoints, and business rules evolved.
@@ -57,7 +58,11 @@ Use only the tools available to you. Prefer built-in filesystem discovery tools
 Run discipline:
 - ${output.filesystemRootInstruction}
 - Never pass host absolute paths like /Users/... to filesystem tools; that creates nested paths inside the repo instead of touching the intended file.
-- Shell execute commands run on the host. If you use execute, run commands from the current runtime root unless a source-specific instruction explicitly tells you to inspect a connector raw file or configured local repository path.
+- ${
+    shellRestricted
+      ? "Shell execute is restricted to a few read-only maintenance commands. Use the structured filesystem tools for repository inspection and documentation writes."
+      : "Shell execute commands run on the host. If you use execute, run commands from the current runtime root unless a source-specific instruction explicitly tells you to inspect a connector raw file or configured local repository path."
+  }
 - Do not exhaustively read every file. For a local knowledge wiki, inspect the existing wiki structure and only the relevant connector evidence or configured local repository paths. For an explicit repository source, inspect the repository tree, package/config files, README-style files, entrypoints, routing files, database/schema files, and representative files for each major domain.
 ${discoveryHint}
 - Prefer grep/glob and short targeted reads over full-file reads when files are large.
@@ -203,7 +208,7 @@ Section quality rules:
 Required documentation structure:
 - ${output.quickstartPath} must be the entrypoint.
 - ${output.quickstartPath} must include a high-level overview and links to every major section.
-- When writing required documentation with filesystem tools or narrow shell execute, use ${output.writePathExample}.
+- When writing required documentation with filesystem tools, use ${output.writePathExample}.
 - ${output.sectionDirectoryInstruction}
 - Each section directory should contain focused Markdown pages; if a directory would contain only one short page, prefer a broader page or a heading in ${output.quickstartPath}.
 - Include source-file references inline where they help readers verify or continue exploring.
diff --git a/test/docs-only-backend.test.ts b/test/docs-only-backend.test.ts
index 17f4db0a..83287f3d 100644
--- a/test/docs-only-backend.test.ts
+++ b/test/docs-only-backend.test.ts
@@ -65,6 +65,22 @@ describe("OpenWikiLocalShellBackend", () => {
     await expect(
       readFile(path.join(rootDir, "AGENTS.md"), "utf8"),
     ).rejects.toThrow();
+
+    for (const command of [
+      "echo bad > AGENTS.md",
+      "pwd && echo bad > AGENTS.md",
+      "git rev-parse HEAD > AGENTS.md",
+    ]) {
+      const shellWrite = await backend.execute(command);
+      expect(shellWrite.exitCode).toBe(1);
+      expect(shellWrite.output).toContain("repository init/update");
+    }
+    await expect(
+      readFile(path.join(rootDir, "AGENTS.md"), "utf8"),
+    ).rejects.toThrow();
+
+    const allowedReadOnlyCommand = await backend.execute("pwd");
+    expect(allowedReadOnlyCommand.exitCode).toBe(0);
   });
 
   test("allows local-wiki init/update writes at the wiki virtual root", async () => {
@@ -83,6 +99,10 @@ describe("OpenWikiLocalShellBackend", () => {
     await expect(
       readFile(path.join(rootDir, "quickstart.md"), "utf8"),
     ).resolves.toBe("updated");
+
+    const execute = await backend.execute("echo shell-available");
+    expect(execute.exitCode).toBe(0);
+    expect(execute.output).toContain("shell-available");
   });
 
   test("keeps chat-mode style backends unrestricted when docsOnly is false", async () => {
diff --git a/test/prompt.test.ts b/test/prompt.test.ts
index 16b2eabf..2a9a4415 100644
--- a/test/prompt.test.ts
+++ b/test/prompt.test.ts
@@ -116,6 +116,39 @@ describe("createSystemPrompt filesystem path guidance", () => {
   });
 });
 
+describe("createSystemPrompt shell guidance", () => {
+  for (const command of ["init", "update"] as const) {
+    test(`repository ${command}: directs the agent away from restricted shell discovery and writes`, () => {
+      const prompt = createSystemPrompt(command, "repository");
+
+      expect(prompt).toContain(
+        "Shell execute is restricted to a few read-only maintenance commands",
+      );
+      expect(prompt).toContain(
+        "Use the structured filesystem tools for repository inspection and documentation writes",
+      );
+      expect(prompt).not.toContain("Use git through shell execute");
+      expect(prompt).not.toContain("narrow shell execute");
+    });
+  }
+
+  test("repository chat retains shell discovery", () => {
+    const prompt = createSystemPrompt("chat", "repository");
+
+    expect(prompt).toContain("Use git through shell execute");
+    expect(prompt).toContain("Shell execute commands run on the host");
+  });
+
+  test("local-wiki init retains shell access for connector raw files", () => {
+    const prompt = createSystemPrompt("init", "local-wiki");
+
+    expect(prompt).toContain("Shell execute commands run on the host");
+    expect(prompt).not.toContain(
+      "Shell execute is restricted to a few read-only maintenance commands",
+    );
+  });
+});
+
 /**
  * The deterministic post-run pass repairs missing or invalid front matter and
  * tags the page `openwiki_generated`. The prompt must tell the agent that code