docs: upstream multi-session safety, troubleshooting, and config examples

[TimeToBuildBob]

Summary

• Multi-session git safety: Add git safe-commit pattern for concurrent session environments (flock-based wrapper prevents prek stash/restore race conditions)
• Submodule prerequisite: Add callout warning to update gptme-contrib before running pre-commit hooks (prevents false positive link errors)
• Troubleshooting section: Common issues with pre-commit hooks, import errors, context script, and submodule problems
• Config examples: Add commented [plugins], [env], and [mcp] sections to gptme.toml so agents can see what's available
• make help target: Lists all available Makefile targets with descriptions

All patterns upstreamed from Bob's production workspace (1700+ sessions).

Test plan

• Pre-commit hooks pass
• Verify make help output is formatted correctly
• Review troubleshooting steps against current gptme-contrib infrastructure

[TimeToBuildBob]

@greptileai review

[greptile-apps]

Greptile Summary

This PR upstreams several production-tested patterns from a 1700+ session workspace into the template, making it more robust for concurrent multi-agent usage and easier to onboard into.

• Multi-session git safety (bin/git-safe-commit, AGENTS.md): A new flock-based wrapper serializes git commit calls (including pre-commit hooks) to prevent prek's stash/restore cycle from racing with concurrent sessions sharing .git/index. The script is correctly wired as a git sub-command via bin/ and the PATH setup instruction is included.
• Submodule prerequisite (AGENTS.md): Adds a callout to run git submodule update --init --recursive before hooks to prevent false-positive link-check failures from gptme-contrib/lessons/.
• Troubleshooting section (AGENTS.md): Covers the most common failure modes: hook failures, import errors, slow context scripts, and submodule issues. Each section is concise and maps directly to a runnable fix.
• Config examples (gptme.toml): Adds documented [plugins], [env], and [mcp] stanzas so agents can discover what's configurable without reading external docs.
• make help (Makefile): Standard grep+awk pattern makes make self-documenting; help is correctly the first target so it becomes the new default.

One portability note: bin/git-safe-commit depends on flock (part of Linux's util-linux) which is not present on macOS by default. This is unlikely to affect the primary Linux/server use-case but is worth noting for contributors developing on macOS.

Confidence Score: 5/5

• This PR is safe to merge — all changes are additive documentation and tooling with no breaking changes.
• All changes are additive (new script, new docs sections, config examples, Makefile target). The core logic of git-safe-commit is correct and well-commented. Prior reviewer concerns are resolved: the script is now included in bin/, and the TOML section behavior is confirmed safe. The only open item is a minor macOS portability note on flock, which doesn't affect the primary Linux/server deployment target.
• No files require special attention.

Important Files Changed

Filename	Overview
bin/git-safe-commit	New script that serializes concurrent git commits using flock to prevent prek stash/restore race conditions. Logic is sound; minor portability concern as flock is Linux-only (not available on macOS without extra tooling).
AGENTS.md	Adds multi-session safety guidance (git safe-commit), submodule prerequisite callout, and a Troubleshooting section. All advice is clear and actionable; the bin/git-safe-commit script is now included in the PR, resolving the prior missing-file concern.
Makefile	Adds a standard help target using grep+awk to list all annotated targets. The help target is correctly placed first so make with no arguments shows available commands. Properly added to .PHONY.
gptme.toml	Adds commented-out [plugins], [env], and [mcp] example sections. [plugins] and [env] headers are intentionally active (gptme handles them safely as empty tables), while [mcp] is fully commented because an active but empty [[mcp.servers]] array would cause parse errors.

Sequence Diagram

sequenceDiagram
    participant S1 as Session 1 (autonomous)
    participant S2 as Session 2 (operator)
    participant FL as flock (commit.lock)
    participant PK as prek (pre-commit runner)
    participant GI as .git/index

    S1->>FL: git safe-commit — acquire lock
    FL-->>S1: lock acquired
    S1->>GI: git add file1.py
    S1->>PK: run pre-commit hooks
    PK->>GI: stash unstaged changes
    Note over S2,FL: S2 tries to commit concurrently
    S2->>FL: git safe-commit — acquire lock (blocked, timeout=60s)
    FL-->>S2: waiting...
    PK-->>GI: restore stashed changes
    S1->>GI: git commit
    S1->>FL: release lock
    FL-->>S2: lock acquired
    S2->>GI: git add file2.py
    S2->>PK: run pre-commit hooks (safe, no index conflict)
    S2->>GI: git commit
    S2->>FL: release lock

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_{Reviews (2): Last reviewed commit: "fix(template): add bin/git-safe-commit a..." | Re-trigger Greptile}

[TimeToBuildBob]

Greptile review addressed

P2 (git safe-commit not in template) — Fixed in a8c4adf:

• Added bin/git-safe-commit (flock-based wrapper) to the template
• Updated AGENTS.md to note that bin/ must be in PATH (e.g. via .envrc)

P1 (empty [plugins]/[env] sections may cause parse errors) — False positive:

• Checked gptme's config parser (gptme/config/models.py): both sections are explicitly handled via config_data.pop("plugins", {}) and config_data.pop("env", {}), so empty tables are perfectly safe
• [mcp] is fully commented because [[mcp.servers]] array tables would error if the header is active but empty — [plugins]/[env] don't have that issue

[TimeToBuildBob]

@greptileai review

[greptile-apps]

flock is Linux-only — not available on macOS by default

flock is part of util-linux and is not installed on macOS out of the box. Developers working on this template from a Mac (or running the CI on macOS) will see flock: command not found and the script will fail completely.

Consider adding a guard at the top that provides a meaningful error message:

Suggested change

	exec flock --timeout 60 "$LOCKFILE" git commit "$@"
	if ! command -v flock &>/dev/null; then
	echo "error: 'flock' is required but not found (Linux: util-linux; macOS: brew install util-linux)" >&2
	exit 1
	fi
	# Serialize commits with 60s timeout (prek hooks can take ~30s)
	exec flock --timeout 60 "$LOCKFILE" git commit "$@"

Alternatively, add a note in the script header documenting the dependency on Linux.