diff --git a/src/constants/hermesagent-paths.ts b/src/constants/hermesagent-paths.ts
index a1f9a451f..b7297b2f8 100644
--- a/src/constants/hermesagent-paths.ts
+++ b/src/constants/hermesagent-paths.ts
@@ -20,9 +20,8 @@ export const HERMESAGENT_RULE_FILE_NAME = ".hermes.md";
 export const HERMESAGENT_GLOBAL_DIR = ".hermes";
 
 /** MCP servers and other settings live in `config.yaml` under `~/.hermes/`. */
-export const HERMESAGENT_MCP_FILE_NAME = "config.yaml";
-export const HERMESAGENT_SOUL_FILE_NAME = "SOUL.md";
 export const HERMESAGENT_CONFIG_FILE_NAME = "config.yaml";
+export const HERMESAGENT_SOUL_FILE_NAME = "SOUL.md";
 export const HERMESAGENT_SOUL_FILE_PATH = join(HERMESAGENT_GLOBAL_DIR, HERMESAGENT_SOUL_FILE_NAME);
 export const HERMESAGENT_CONFIG_FILE_PATH = join(
   HERMESAGENT_GLOBAL_DIR,
diff --git a/src/e2e/e2e-commands.spec.ts b/src/e2e/e2e-commands.spec.ts
index 1cbdc0475..f430d76ab 100644
--- a/src/e2e/e2e-commands.spec.ts
+++ b/src/e2e/e2e-commands.spec.ts
@@ -213,6 +213,9 @@ describe("E2E: commands (global mode)", () => {
     { target: "factorydroid", outputPath: join(".factory", "commands", "review-pr.md") },
     { target: "goose", outputPath: join(".config", "goose", "recipes", "review-pr.yaml") },
     { target: "qwencode", outputPath: join(".qwen", "commands", "review-pr.md") },
+    // Hermes Agent has no project-scoped command location; commands are emitted
+    // as Hermes skills under ~/.hermes/skills/<slug>/SKILL.md (global only).
+    { target: "hermesagent", outputPath: join(".hermes", "skills", "review-pr", "SKILL.md") },
   ])("should generate $target commands in home directory", async ({ target, outputPath }) => {
     const projectDir = getProjectDir();
     const homeDir = getHomeDir();
diff --git a/src/e2e/e2e-hooks.spec.ts b/src/e2e/e2e-hooks.spec.ts
index 78da67ae9..e420cce01 100644
--- a/src/e2e/e2e-hooks.spec.ts
+++ b/src/e2e/e2e-hooks.spec.ts
@@ -633,4 +633,40 @@ describe("E2E: hooks (global mode)", () => {
     const configContent = await readFileContent(join(homeDir, ".vibe", "config.toml"));
     expect(configContent).toContain("enable_experimental_hooks = true");
   });
+
+  it("should generate hermesagent hooks in home directory", async () => {
+    const projectDir = getProjectDir();
+    const homeDir = getHomeDir();
+
+    // Hermes Agent has no project-scoped hooks location; hooks are merged under
+    // the `hooks.rulesync` key of the shared global ~/.hermes/config.yaml (YAML,
+    // global only).
+    const hooksContent = JSON.stringify(
+      {
+        version: 1,
+        root: true,
+        hooks: {
+          sessionStart: [{ type: "command", command: ".rulesync/hooks/session-start.sh" }],
+          stop: [{ command: ".rulesync/hooks/audit.sh" }],
+        },
+      },
+      null,
+      2,
+    );
+    await writeFileContent(join(projectDir, RULESYNC_HOOKS_RELATIVE_FILE_PATH), hooksContent);
+
+    await runGenerate({
+      target: "hermesagent",
+      features: "hooks",
+      global: true,
+      env: { HOME_DIR: homeDir },
+    });
+
+    // The config is YAML; assert the canonical hook command paths survive
+    // generation under the nested `hooks.rulesync` block.
+    const generatedContent = await readFileContent(join(homeDir, ".hermes", "config.yaml"));
+    expect(generatedContent).toContain("rulesync");
+    expect(generatedContent).toContain(".rulesync/hooks/session-start.sh");
+    expect(generatedContent).toContain(".rulesync/hooks/audit.sh");
+  });
 });
diff --git a/src/e2e/e2e-permissions.spec.ts b/src/e2e/e2e-permissions.spec.ts
index 1870ff497..8397aac8d 100644
--- a/src/e2e/e2e-permissions.spec.ts
+++ b/src/e2e/e2e-permissions.spec.ts
@@ -1603,6 +1603,54 @@ describe("E2E: permissions (global mode)", () => {
     // Unrelated user settings preserved by the non-destructive merge.
     expect(parsed.model).toBe("claude-sonnet");
   });
+
+  it("should generate hermesagent permissions in home directory with --global", async () => {
+    const projectDir = getProjectDir();
+    const homeDir = getHomeDir();
+
+    await writeFileContent(
+      join(projectDir, RULESYNC_PERMISSIONS_RELATIVE_FILE_PATH),
+      JSON.stringify(
+        {
+          permission: {
+            bash: { "git status *": "allow", "rm -rf *": "deny" },
+          },
+        },
+        null,
+        2,
+      ),
+    );
+
+    // Pre-seed config.yaml with unrelated user settings to verify the
+    // non-destructive merge into ~/.hermes/config.yaml.
+    await writeFileContent(
+      join(homeDir, ".hermes", "config.yaml"),
+      ["model: hermes-large", "terminal: tmux"].join("\n"),
+    );
+
+    await runGenerate({
+      target: "hermesagent",
+      features: "permissions",
+      global: true,
+      env: { HOME_DIR: homeDir },
+    });
+
+    // Hermes Agent has no project-scoped permissions location; permissions are
+    // merged into the shared global ~/.hermes/config.yaml. Allow rules are also
+    // surfaced as a flat `command_allowlist`, and the canonical map is preserved
+    // under `permissions.rulesync` for round-tripping.
+    const parsed = toTable(load(await readFileContent(join(homeDir, ".hermes", "config.yaml"))));
+    expect(parsed.command_allowlist).toEqual(["git status *"]);
+    const permissions = toTable(parsed.permissions);
+    const rulesyncProfile = toTable(permissions.rulesync);
+    const permissionMap = toTable(rulesyncProfile.permission);
+    const bash = toTable(permissionMap.bash);
+    expect(bash["git status *"]).toBe("allow");
+    expect(bash["rm -rf *"]).toBe("deny");
+    // Unrelated user settings preserved by the non-destructive merge.
+    expect(parsed.model).toBe("hermes-large");
+    expect(parsed.terminal).toBe("tmux");
+  });
 });
 
 type AugmentEntry = {
diff --git a/src/e2e/e2e-skills.spec.ts b/src/e2e/e2e-skills.spec.ts
index e1918d312..ed3bfabf3 100644
--- a/src/e2e/e2e-skills.spec.ts
+++ b/src/e2e/e2e-skills.spec.ts
@@ -426,6 +426,11 @@ describe("E2E: skills (global mode)", () => {
       target: "vibe",
       outputPath: join(".vibe", "skills", "test-skill", "SKILL.md"),
     },
+    {
+      // Hermes Agent reads skills from ~/.hermes/skills/ (global only).
+      target: "hermesagent",
+      outputPath: join(".hermes", "skills", "test-skill", "SKILL.md"),
+    },
   ])("should generate $target skills in home directory", async ({ target, outputPath }) => {
     const projectDir = getProjectDir();
     const homeDir = getHomeDir();
diff --git a/src/e2e/e2e-subagents.spec.ts b/src/e2e/e2e-subagents.spec.ts
index 7f7fad1fb..e8c9791f7 100644
--- a/src/e2e/e2e-subagents.spec.ts
+++ b/src/e2e/e2e-subagents.spec.ts
@@ -470,6 +470,13 @@ describe("E2E: subagents (global mode)", () => {
       target: "goose",
       outputPath: join(".config", "goose", "recipes", "subagents", "planner.yaml"),
     },
+    {
+      // Hermes Agent has no project-scoped subagent location; subagents are
+      // emitted as JSON specs under ~/.hermes/rulesync/subagents/<slug>.json,
+      // discovered by the generated rulesync-subagents plugin (global only).
+      target: "hermesagent",
+      outputPath: join(".hermes", "rulesync", "subagents", "planner.json"),
+    },
   ])("should generate $target subagents in home directory", async ({ target, outputPath }) => {
     const projectDir = getProjectDir();
     const homeDir = getHomeDir();
diff --git a/src/features/commands/hermesagent-command.ts b/src/features/commands/hermesagent-command.ts
index 6974315ba..7bde1d853 100644
--- a/src/features/commands/hermesagent-command.ts
+++ b/src/features/commands/hermesagent-command.ts
@@ -42,8 +42,7 @@ export class HermesagentCommand extends ToolCommand {
   }
 
   constructor({ slug, ...params }: HermesagentCommandParams) {
-    const resolvedSlug =
-      slug ?? basename(dirname(params.relativeDirPath)) ?? commandSlug(params.relativeFilePath);
+    const resolvedSlug = slug ?? basename(dirname(params.relativeDirPath));
     super({
       ...params,
       ...HermesagentCommand.getSettablePaths({ slug: resolvedSlug }),
diff --git a/src/features/mcp/hermesagent-mcp.ts b/src/features/mcp/hermesagent-mcp.ts
index 02c26b3f3..968404a96 100644
--- a/src/features/mcp/hermesagent-mcp.ts
+++ b/src/features/mcp/hermesagent-mcp.ts
@@ -1,20 +1,18 @@
 import { join } from "node:path";
 
-import { dump, load } from "js-yaml";
-
 import {
+  HERMESAGENT_CONFIG_FILE_NAME,
   HERMESAGENT_GLOBAL_DIR,
-  HERMESAGENT_MCP_FILE_NAME,
 } from "../../constants/hermesagent-paths.js";
 import { ValidationResult } from "../../types/ai-file.js";
 import { McpServers } from "../../types/mcp.js";
-import { formatError } from "../../utils/error.js";
 import { readFileContentOrNull, readOrInitializeFileContent } from "../../utils/file.js";
 import {
   omitPrototypePollutionKeys,
   PROTOTYPE_POLLUTION_KEYS,
 } from "../../utils/prototype-pollution.js";
 import { isPlainObject, isRecord, isStringArray } from "../../utils/type-guards.js";
+import { parseHermesConfig, stringifyHermesConfig } from "../hermes-config.js";
 import { RulesyncMcp } from "./rulesync-mcp.js";
 import {
   ToolMcp,
@@ -28,32 +26,6 @@ import {
 const HERMESAGENT_GLOBAL_ONLY_MESSAGE =
   "Hermes Agent MCP is global-only; use --global to sync ~/.hermes/config.yaml";
 
-function parseHermesConfig(
-  fileContent: string,
-  relativeDirPath: string,
-  relativeFilePath: string,
-): Record<string, unknown> {
-  const configPath = join(relativeDirPath, relativeFilePath);
-  let parsed: unknown;
-  try {
-    parsed = load(fileContent);
-  } catch (error) {
-    throw new Error(`Failed to parse Hermes config at ${configPath}: ${formatError(error)}`, {
-      cause: error,
-    });
-  }
-  // An empty config.yaml parses to undefined/null; treat it as an empty object.
-  if (parsed === undefined || parsed === null) {
-    return {};
-  }
-  // `isPlainObject` (not `isRecord`) rejects class instances for
-  // prototype-pollution hardening; a YAML mapping always parses to a plain object.
-  if (!isPlainObject(parsed)) {
-    throw new Error(`Failed to parse Hermes config at ${configPath}: expected a YAML mapping`);
-  }
-  return parsed;
-}
-
 /**
  * Resolves the canonical remote URL for a server (`url` or the `httpUrl` alias).
  */
@@ -185,15 +157,7 @@ export class HermesagentMcp extends ToolMcp {
 
   constructor(params: ToolMcpParams) {
     super(params);
-    if (this.fileContent !== undefined) {
-      this.config = parseHermesConfig(
-        this.fileContent,
-        this.relativeDirPath,
-        this.relativeFilePath,
-      );
-    } else {
-      this.config = {};
-    }
+    this.config = this.fileContent !== undefined ? parseHermesConfig(this.fileContent) : {};
   }
 
   getConfig(): Record<string, unknown> {
@@ -205,7 +169,7 @@ export class HermesagentMcp extends ToolMcp {
   }
 
   override setFileContent(fileContent: string): void {
-    const config = parseHermesConfig(fileContent, this.relativeDirPath, this.relativeFilePath);
+    const config = parseHermesConfig(fileContent);
     const mcpServers = isRecord(this.config.mcp_servers) ? this.config.mcp_servers : {};
     const merged = mergeHermesMcpServers(
       config,
@@ -213,7 +177,7 @@ export class HermesagentMcp extends ToolMcp {
     );
 
     this.config = merged;
-    super.setFileContent(dump(merged));
+    super.setFileContent(stringifyHermesConfig(merged));
   }
 
   override isDeletable(): boolean {
@@ -225,7 +189,7 @@ export class HermesagentMcp extends ToolMcp {
   static getSettablePaths(_options?: { global?: boolean }): ToolMcpSettablePaths {
     return {
       relativeDirPath: HERMESAGENT_GLOBAL_DIR,
-      relativeFilePath: HERMESAGENT_MCP_FILE_NAME,
+      relativeFilePath: HERMESAGENT_CONFIG_FILE_NAME,
     };
   }
 
@@ -266,7 +230,7 @@ export class HermesagentMcp extends ToolMcp {
       join(outputRoot, paths.relativeDirPath, paths.relativeFilePath),
       "",
     );
-    const config = parseHermesConfig(fileContent, paths.relativeDirPath, paths.relativeFilePath);
+    const config = parseHermesConfig(fileContent);
 
     // Merge the `mcp_servers:` block into the shared config, preserving other
     // keys (model, terminal, ...).
@@ -279,7 +243,7 @@ export class HermesagentMcp extends ToolMcp {
       outputRoot,
       relativeDirPath: paths.relativeDirPath,
       relativeFilePath: paths.relativeFilePath,
-      fileContent: dump(merged),
+      fileContent: stringifyHermesConfig(merged),
       validate,
       global,
     });
diff --git a/src/features/skills/hermesagent-skill.test.ts b/src/features/skills/hermesagent-skill.test.ts
new file mode 100644
index 000000000..ea237e9e0
--- /dev/null
+++ b/src/features/skills/hermesagent-skill.test.ts
@@ -0,0 +1,104 @@
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+import { HERMESAGENT_SKILLS_DIR_PATH } from "../../constants/hermesagent-paths.js";
+import { RULESYNC_SKILLS_RELATIVE_DIR_PATH } from "../../constants/rulesync-paths.js";
+import { setupTestDirectory } from "../../test-utils/test-directories.js";
+import { HermesagentSkill } from "./hermesagent-skill.js";
+import { RulesyncSkill } from "./rulesync-skill.js";
+
+describe("HermesagentSkill", () => {
+  let testDir: string;
+  let cleanup: () => Promise<void>;
+
+  beforeEach(async () => {
+    const testSetup = await setupTestDirectory();
+    testDir = testSetup.testDir;
+    cleanup = testSetup.cleanup;
+    vi.spyOn(process, "cwd").mockReturnValue(testDir);
+  });
+
+  afterEach(async () => {
+    await cleanup();
+    vi.restoreAllMocks();
+  });
+
+  describe("getSettablePaths", () => {
+    it("should return the Hermes skills directory as relativeDirPath", () => {
+      const paths = HermesagentSkill.getSettablePaths();
+      expect(paths.relativeDirPath).toBe(HERMESAGENT_SKILLS_DIR_PATH);
+    });
+  });
+
+  describe("constructor", () => {
+    it("should force the Hermes skills directory even when another relativeDirPath is passed", () => {
+      const skill = new HermesagentSkill({
+        outputRoot: testDir,
+        relativeDirPath: "ignored",
+        dirName: "test-skill",
+        frontmatter: {
+          name: "Test Skill",
+          description: "Test skill description",
+        },
+        body: "This is the body of the Hermes skill.",
+        validate: true,
+      });
+
+      expect(skill).toBeInstanceOf(HermesagentSkill);
+      expect(skill.getRelativeDirPath()).toBe(HERMESAGENT_SKILLS_DIR_PATH);
+      expect(skill.getBody()).toBe("This is the body of the Hermes skill.");
+      expect(skill.getFrontmatter()).toEqual({
+        name: "Test Skill",
+        description: "Test skill description",
+      });
+    });
+  });
+
+  describe("fromRulesyncSkill", () => {
+    it("should create an instance routed to the Hermes skills directory", () => {
+      const rulesyncSkill = new RulesyncSkill({
+        outputRoot: testDir,
+        relativeDirPath: RULESYNC_SKILLS_RELATIVE_DIR_PATH,
+        dirName: "test-skill",
+        frontmatter: {
+          name: "Test Skill",
+          description: "Test skill description",
+        },
+        body: "Test body content",
+        validate: true,
+      });
+
+      const skill = HermesagentSkill.fromRulesyncSkill({ rulesyncSkill, global: true });
+
+      expect(skill).toBeInstanceOf(HermesagentSkill);
+      expect(skill.getRelativeDirPath()).toBe(HERMESAGENT_SKILLS_DIR_PATH);
+      expect(skill.getBody()).toBe("Test body content");
+      expect(skill.getFrontmatter()).toEqual({
+        name: "Test Skill",
+        description: "Test skill description",
+      });
+    });
+  });
+
+  describe("toRulesyncSkill", () => {
+    it("should convert back to a RulesyncSkill", () => {
+      const skill = new HermesagentSkill({
+        outputRoot: testDir,
+        dirName: "test-skill",
+        frontmatter: {
+          name: "Test Skill",
+          description: "Test description",
+        },
+        body: "Test body",
+        validate: true,
+      });
+
+      const rulesyncSkill = skill.toRulesyncSkill();
+
+      expect(rulesyncSkill.getFrontmatter()).toMatchObject({
+        name: "Test Skill",
+        description: "Test description",
+      });
+      expect(rulesyncSkill.getBody()).toBe("Test body");
+    });
+  });
+});
diff --git a/src/lib/generate.ts b/src/lib/generate.ts
index 5aceab479..49ae59633 100644
--- a/src/lib/generate.ts
+++ b/src/lib/generate.ts
@@ -145,7 +145,7 @@ async function processFeatureWithRulesyncFiles(params: {
   if (rulesyncFiles.length === 0) {
     return processEmptyFeatureGeneration({ config, processor, skipFilePaths });
   }
-  let toolFiles = await processor.convertRulesyncFilesToToolFiles(rulesyncFiles);
+  const toolFiles = await processor.convertRulesyncFilesToToolFiles(rulesyncFiles);
   return processFeatureGeneration({ config, processor, toolFiles, skipFilePaths });
 }
 
diff --git a/src/types/feature-processor.test.ts b/src/types/feature-processor.test.ts
index 89cc2cd04..7b7fc811d 100644
--- a/src/types/feature-processor.test.ts
+++ b/src/types/feature-processor.test.ts
@@ -23,6 +23,8 @@ function createMockFile(filePath: string): AiFile {
     getFilePath: () => filePath,
     getFileContent: () => "content",
     getRelativePathFromCwd: () => filePath,
+    // Declared on the AiFile base class; defaults to false for non-merging files.
+    shouldMergeExistingFileContent: () => false,
   } as AiFile;
 }
 
diff --git a/src/types/feature-processor.ts b/src/types/feature-processor.ts
index 2d3b0fbdc..4dc459d29 100644
--- a/src/types/feature-processor.ts
+++ b/src/types/feature-processor.ts
@@ -63,12 +63,7 @@ export abstract class FeatureProcessor {
       const filePath = aiFile.getFilePath();
       const existingFileContent = await readFileContentOrNull(filePath);
 
-      if (
-        existingFileContent !== null &&
-        "shouldMergeExistingFileContent" in aiFile &&
-        typeof aiFile.shouldMergeExistingFileContent === "function" &&
-        aiFile.shouldMergeExistingFileContent()
-      ) {
+      if (existingFileContent !== null && aiFile.shouldMergeExistingFileContent()) {
         aiFile.setFileContent(existingFileContent);
       }