[bilersan]

Summary

ctx init wrote the agent bootstrap instructions only to CLAUDE.md, while
ctx setup codex|opencode|pi deployed a second, older AGENTS.md template:
mixed-tool teams carried two diverging texts and non-Claude users got nothing
from ctx init. AGENTS.md is the vendor-neutral
instruction file (stewarded by the Agentic AI Foundation under the Linux
Foundation, announced 2025-12-09)
read natively by Codex, Copilot, Cursor, Gemini CLI, OpenCode, Pi and, since
Claude Code 2.1.277, by
Claude Code. This PR makes ctx init create or merge AGENTS.md from the one
template every agent shares, and turns the ctx block of CLAUDE.md into an
@AGENTS.md import. The bridge stays because Claude Code's own AGENTS.md
fallback needs 2.1.277, is unavailable in some sessions, and switches off as
soon as any CLAUDE.md exists in the tree, which is exactly the --merge
case. Existing projects migrate with ctx init --reset --merge.

Closes #197

Changes

• internal/cli/initialize/core/agents: new HandleMd, wired into ctx init
  before the CLAUDE.md handler; failures stay non-fatal, as for CLAUDE.md
  — serves specs/init-agents-md.md
• internal/assets/integrations/agents.md: tool-neutral version of the former
  CLAUDE.md content between <!-- ctx:agents --> and the new
  marker.AgentsEnd (<!-- ctx:agents:end -->); ctx setup agents|codex|opencode|pi
  ship the same file and already skip on the marker — serves specs/init-agents-md.md
• internal/assets/claude/CLAUDE.md: reduced to the marker-bounded @AGENTS.md
  import — serves specs/init-agents-md.md
• merge.OrCreate inserts only the marker-bounded block into an existing file
  (the template's own # Project Context title used to come along as a second
  H1); block extraction moves to merge/section.go, shared with
  UpdateMarkedSection — serves specs/init-agents-md.md
• Docs (docs/cli/init-status.md, docs/cli/setup.md, docs/operations/{migration,integrations,upgrading}.md,
  docs/operations/runbooks/breaking-migration.md, docs/home/{common-workflows,configuration}.md),
  ctx init long help and --merge flag text, internal/assets/README.md
  and package doc comments follow the new output — serves specs/init-agents-md.md
• .context/DECISIONS.md: records the choice and supersedes the 2026-01-25
  "Removed AGENTS.md from project root" entry — serves specs/init-agents-md.md

Specs

• specs/init-agents-md.md — ctx init output for AGENTS.md and the
  CLAUDE.md bridge: behavior table for fresh, hand-written and already
  marked files, --merge/--reset semantics, non-goals (setup deploy logic,
  repo-root flip, nested AGENTS.md, copilot-instructions)

Verification

• gofmt, go vet ./... and golangci-lint v2.15.0 (the CI pin): clean, 0 issues
• go test ./... on a Windows checkout: no new failures against a clean
  upstream/main worktree run the same way (the pre-existing environment
  failures are identical in both runs); internal/cli/initialize at 100%
  statement coverage; internal/audit and internal/compliance conventions
  pass for the new files
• Hand-driven ctx init --merge against a project with its own AGENTS.md
  and CLAUDE.md: block inserted after each H1, backups written, the rest
  untouched; a fresh ctx init creates both files from the templates
• Not run locally: make check-steering (the branch touches no steering
  sources or outputs); CI covers it