fix automake portability error and add basic AI agent config

[aspiers]

Also .editorconfig. Too rushed to split these into separate PRs, sorry!

Summary by CodeRabbit

• New Features
  • Added AI permissions configuration enabling specific GitHub issue, web fetch (unix.stackexchange.com), and Bash actions.
• Documentation
  • Added an AI agents guide covering repository structure, build/test workflows, and development practices; updated assistant-facing docs to reference it.
• Style
  • Introduced a project-wide editor config for consistent formatting and clarified build output messages.
• Chores
  • Bumped build tooling target to Automake 1.18.x and updated distribution ignores to exclude AI agent config artifacts.

[coderabbitai]

Walkthrough

Adds EditorConfig and a Claude settings JSON for AI-agent permissions, new AI-assistant documentation files (AGENTS.md, CLAUDE.md, GEMINI.md), tweaks Makefile.am user messages, updates aclocal.m4 to target Automake 1.18.1 with new private helpers and sanity/silent-rule adjustments, and extends MANIFEST.SKIP to exclude agent artifacts. No runtime application logic changes.

Changes

Cohort / File(s)	Summary
Repo formatting & AI agent settings /.editorconfig, /.claude/settings.json	Add EditorConfig (UTF‑8, LF, final newline, trim trailing whitespace, language-specific indent rules) and .claude/settings.json with a permissions object: allow list (specific GitHub issue actions, WebFetch(domain:unix.stackexchange.com), and several Bash(...) commands) and an empty deny list.
AI assistant docs /AGENTS.md, /CLAUDE.md, /GEMINI.md	Add AGENTS.md (developer guidance for AI assistants: repo layout, build/test/install, core class responsibilities, workflows and editing .in files); add/update CLAUDE.md and GEMINI.md alongside docs. Documentation-only changes.
Makefile messages /Makefile.am	Adjust check_pmdir output lines to emit plain-text messages instead of comment-prefixed lines; control flow and conditionals retained.
Automake macros / build tooling /aclocal.m4	Bump Automake API/target to 1.18 / 1.18.1; introduce private helpers (_AM_PROG_RM_F, _AM_PROG_XARGS_N, _AM_SLEEP_FRACTIONAL_SECONDS, _AM_FILESYSTEM_TIMESTAMP_RESOLUTION, _AM_SILENT_RULES) and AM_RUN_LOG; rewire AM_SANITY_CHECK and silent-rule handling to use private helpers; adjust tar selection logic and metadata/year headers.
Distribution manifest /MANIFEST.SKIP	Add skip patterns to exclude AI agent config/docs: AGENTS.md, CLAUDE.md, GEMINI.md, and the .claude/ directory.

Sequence Diagram(s)

sequenceDiagram
  autonumber
  actor Dev as Developer
  participant Cfg as ./configure
  participant AM as aclocal.m4 (Automake v1.18.1)
  participant FS as Filesystem
  participant Mk as make (Makefile.am)

  Dev->>Cfg: run ./configure
  Cfg->>AM: invoke AM_* macros (updated to v1.18.1)
  AM->>AM: initialize _AM_SILENT_RULES and AM_SANITY_CHECK
  AM->>FS: probe _AM_FILESYSTEM_TIMESTAMP_RESOLUTION / _AM_SLEEP_FRACTIONAL_SECONDS
  AM-->>Cfg: emit configured build rules
  Dev->>Mk: run make
  Mk-->>Dev: produce build output (user-facing messages updated)

Loading

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~60 minutes

Poem

A rabbit nudges files with bright little hops,
New rules and macros tumble into neat crops.
Docs like clover, whitespace trimmed fine,
Configure hums softly—Automake sings 1.18.
Carrots in Make, and the build feels sublime. 🥕✨

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	Title clearly and succinctly describes the two primary changes—resolving an automake portability issue and introducing a basic AI agent configuration—both of which are directly reflected in the build script updates and the new agent config files, making it an accurate summary of the pull request’s scope.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch misc-updates

---

📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 3674bf6 and f2c30a3.

📒 Files selected for processing (8)

• .claude/settings.json (1 hunks)
• .editorconfig (1 hunks)
• AGENTS.md (1 hunks)
• CLAUDE.md (1 hunks)
• GEMINI.md (1 hunks)
• MANIFEST.SKIP (1 hunks)
• Makefile.am (1 hunks)
• aclocal.m4 (19 hunks)

✅ Files skipped from review due to trivial changes (1)

• .editorconfig

🚧 Files skipped from review as they are similar to previous changes (3)

• CLAUDE.md
• GEMINI.md
• .claude/settings.json

🔇 Additional comments (3)

Makefile.am (1)

133-142: LGTM!

The message formatting changes improve readability by removing the comment-style prefix from user-facing output. The logic remains unchanged.

aclocal.m4 (1)

1-1: Version bump looks correct.

The update from Automake 1.16.5 to 1.18.1 is consistent throughout the file (lines 1, 35, 38, 54). The new private helpers (_AM_PROG_RM_F, AM_RUN_LOG, _AM_SLEEP_FRACTIONAL_SECONDS, _AM_FILESYSTEM_TIMESTAMP_RESOLUTION, _AM_SILENT_RULES, _AM_PROG_XARGS_N) and refactored logic are standard updates from the newer Automake version.

Also applies to: 35-35, 54-54

AGENTS.md (1)

1-166: Excellent documentation for AI assistants!

This comprehensive guide covers all essential aspects of working with the GNU Stow codebase:

• Clear emphasis on the critical .in file preprocessing requirement
• Well-organized development workflows (build, test, install)
• Detailed architecture overview with key classes and design principles
• Practical test structure and common patterns
• Helpful debugging and workflow tips

The documentation is accurate, well-structured, and provides valuable context for AI coding assistants.

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[coderabbitai]

Actionable comments posted: 3

🧹 Nitpick comments (4)

GEMINI.md (1)

1-1: Clarify the purpose of this file.

This file only contains "AGENTS.md" as text, which is unclear. If this is intended as a redirect or reference to AGENTS.md, consider either:

1. Creating a proper markdown link: See [AGENTS.md](AGENTS.md) for guidance.
2. Using a symbolic link instead of a file
3. Adding explanatory text about why GEMINI.md points to AGENTS.md

The current content may confuse readers who open this file expecting Gemini-specific guidance.

Makefile.am (1)

131-143: LGTM! Output formatting improvement.

The changes improve the user-facing output by converting comment-style messages to plain text. This makes the installation messages clearer without changing the underlying logic or functionality.

AGENTS.md (1)

1-166: Excellent comprehensive documentation!

This is well-written guidance for AI coding assistants that covers all critical aspects of the repository:

Strengths:

• Clear emphasis on the .in file preprocessing requirement (lines 21-41) - this is crucial
• Comprehensive coverage of build, test, and installation commands
• Good architectural overview of core classes and design principles
• Practical examples of common development patterns
• Accurate technical details throughout

Minor suggestion: Consider adding a section about the MANIFEST file and how to keep it in sync, given the pipeline failure in this PR. Something like:

### Distribution Manifest

The MANIFEST file lists all files to be included in distributions. After adding new files, update it by running:

\`\`\`bash
make manifest
# or manually edit MANIFEST to add/remove files
\`\`\`

Files matching patterns in MANIFEST.SKIP are automatically excluded.

CLAUDE.md (1)

1-1: Clarify the purpose of this file.

This file only contains "AGENTS.md" as text, which is unclear. This is the same pattern as GEMINI.md. If these files are intended as redirects or references to AGENTS.md, consider:

1. Creating a proper markdown link: See [AGENTS.md](AGENTS.md) for guidance.
2. Using symbolic links instead of separate files
3. Adding explanatory text about why AI-agent-specific files point to a common AGENTS.md

The current approach may confuse readers who open CLAUDE.md or GEMINI.md expecting agent-specific guidance.

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 5045fef and 3674bf6.

📒 Files selected for processing (8)

• .claude/settings.json (1 hunks)
• .editorconfig (1 hunks)
• AGENTS.md (1 hunks)
• CLAUDE.md (1 hunks)
• GEMINI.md (1 hunks)
• MANIFEST.SKIP (1 hunks)
• Makefile.am (1 hunks)
• aclocal.m4 (19 hunks)

🧰 Additional context used

🪛 GitHub Actions: Test suite

MANIFEST.SKIP

[error] 1-1: Not in MANIFEST: .editorconfig

---

[error] 2-2: MANIFEST appears to be out of sync with the distribution

🔇 Additional comments (2)

.claude/settings.json (1)

1-17: LGTM! Safe and appropriate permissions.

The permissions configuration is well-scoped for an AI agent working with this repository:

• GitHub API access (read-only for issues/comments) supports collaboration workflows
• WebFetch limited to unix.stackexchange.com for documentation/troubleshooting
• Bash commands restricted to read-only operations (cat, grep) and build tools (autoreconf, automake, make, configure)
• No write operations or dangerous commands allowed
• Empty deny list is appropriate (allow-list approach is safer)

The JSON syntax is valid and the structure follows expected schema.

aclocal.m4 (1)

1-1: aclocal.m4 regeneration confirmed
No manual edits detected; git history shows only automated version bumps.