fix(#1098): guard generate-claude-md against clobbering hand-crafted files; redirect default to .claude/CLAUDE.md (#1118)

/gsd-new-project wrote a repo-root CLAUDE.md full of broad project docs,
overwriting/diluting a hand-crafted instruction file. --force was parsed but
silently dropped, and nothing guarded an existing non-GSD file.

- Guard: an existing instruction file with no `<!-- GSD:<section>-start` markers
  (hand-crafted) is left untouched; report action:"skipped". --force (now wired
  through CmdGenerateClaudeMdOptions) overwrites intentionally. The marker check
  uses /<!-- GSD:[a-z]+-start/ so a file merely documenting GSD syntax is safe.
- Redirect: the Claude-family default output is now ./.claude/CLAUDE.md (a valid
  auto-loaded project-memory location) instead of repo-root ./CLAUDE.md. Aligned
  across the handler default, config-defaults.manifest.json, buildNewProjectConfig,
  the config template, new-project.md, and cmdGenerateClaudeProfile; advisory
  read-CLAUDE.md hints in plan-phase/quick/profile-user updated. Codex still
  writes AGENTS.md.

Closes #1098

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

docs/CONFIGURATION.md

@@ -129,7 +129,7 @@ GSD stores project settings in `.planning/config.json`. Created during `/gsd-new
   "intel": {
     "enabled": false
   },
-  "claude_md_path": "./CLAUDE.md"
+  "claude_md_path": "./.claude/CLAUDE.md"
 }
 ```
 
@@ -161,7 +161,7 @@ GSD stores project settings in `.planning/config.json`. Created during `/gsd-new
 | `response_language` | string | language code | (none) | Language for agent responses (e.g., `"pt"`, `"ko"`, `"ja"`). Propagates to all spawned agents for cross-phase language consistency. Added in v1.32 |
 | `context_window` | number | any integer | `200000` | Context window size in tokens. Set `1000000` for 1M-context models (e.g., `claude-fable-5`). Values `>= 500000` enable adaptive context enrichment (full-body reads of prior SUMMARY.md, deeper anti-pattern reads). Configured via `/gsd-config --advanced`. |
 | `context_profile` | string | `dev`, `research`, `review` | (none) | Execution context preset that applies a pre-configured bundle of mode, model, and workflow settings for the current type of work. Added in v1.34 |
-| `claude_md_path` | string | any file path | `./CLAUDE.md` | Custom output path for the generated CLAUDE.md file. Useful for monorepos or projects that need CLAUDE.md in a non-root location. Defaults to `./CLAUDE.md` at the project root. Added in v1.36 |
+| `claude_md_path` | string | any file path | `./.claude/CLAUDE.md` | Custom output path for the generated CLAUDE.md file. Useful for monorepos or projects that need CLAUDE.md in a non-root location. Defaults to `./.claude/CLAUDE.md` — a valid project-scoped memory location that keeps GSD-generated content from polluting a hand-crafted repo-root `CLAUDE.md` ([#1098](https://github.com/open-gsd/gsd-core/issues/1098)). An existing file without GSD markers is never overwritten unless `--force` is passed. Default changed from `./CLAUDE.md` in v1.5. Added in v1.36 |
 | `claude_md_assembly.mode` | enum | `embed`, `link` | `embed` | Controls how managed sections are written into CLAUDE.md. `embed` (default) inlines content between GSD markers. `link` writes `@.planning/<source-path>` instead — Claude Code expands the reference at runtime, reducing CLAUDE.md size by ~65% on typical projects. `link` only applies to sections that have a real source file; `workflow` and fallback sections always embed. Per-block overrides: `claude_md_assembly.blocks.<section>` (e.g. `claude_md_assembly.blocks.architecture: link`). Added in v1.38 |
 | `context` | string | any text | (none) | Custom context string injected into every agent prompt for the project. Use to provide persistent project-specific guidance (e.g., coding conventions, team practices) that every agent should be aware of |
 | `phase_naming` | string | any string | (none) | Custom prefix for phase directory names. When set, overrides the auto-generated phase slug (e.g., `"feature"` produces `feature-01-setup/` instead of the roadmap-derived slug) |

docs/FEATURES.md

@@ -2507,9 +2507,10 @@ Users who run a memory / knowledge-base MCP server (for example, ExoCortex-style
 **Purpose:** Allow projects to store their CLAUDE.md in a non-root location. The `claude_md_path` config key controls where `/gsd-profile-user` and related commands write the generated CLAUDE.md file.
 
 **Requirements:**
-- REQ-CMDPATH-01: `claude_md_path` defaults to `./CLAUDE.md`
+- REQ-CMDPATH-01: `claude_md_path` defaults to `./.claude/CLAUDE.md` (a valid project-scoped memory location; changed from `./CLAUDE.md` in v1.5 per [#1098](https://github.com/open-gsd/gsd-core/issues/1098) so generated content does not pollute a hand-crafted repo-root `CLAUDE.md`)
 - REQ-CMDPATH-02: Profile generation commands read the path from config and write to the specified location
 - REQ-CMDPATH-03: Relative paths are resolved from the project root
+- REQ-CMDPATH-04: `generate-claude-md` never overwrites an existing instruction file that lacks GSD section markers (a hand-crafted file) unless `--force` is passed
 
 **Configuration:** `claude_md_path`