chore: remove deprecated agents-manage-mcp package and simplify MCP scripts

[amikofalvy]

Summary

• Remove the deprecated @inkeep/agents-manage-mcp package (replaced by @inkeep/agents-mcp)
• Remove the /manage/mcp API endpoint (the /mcp endpoint using the new package remains)
• Simplify root MCP scripts to a single mcp:generate command
• Delete stale MCP generator system (scripts/generate-mcp-package.mjs, templates, docs)
• Delete stale Dockerfile.manage-api-test (references non-existent agents-manage-api/)
• Clean up all cross-repo references (build configs, skill files, env scripts)

Test plan

• pnpm install succeeds
• pnpm build passes
• pnpm typecheck passes
• pnpm lint passes
• pnpm test passes
• No remaining references to agents-manage-mcp in codebase
• /mcp endpoint (using agents-mcp) is unaffected

🤖 Generated with Claude Code

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Project	Deployment	Actions	Updated (UTC)
agents-api	Ready	Preview, Comment	Feb 18, 2026 1:09am
agents-docs	Ready	Preview, Comment	Feb 18, 2026 1:09am
agents-manage-ui	Ready	Preview, Comment	Feb 18, 2026 1:09am

[changeset-bot]

⚠️ No Changeset found

Latest commit: fe18a6e

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[claude]

PR Review Summary

(3) Total Issues | Risk: Medium

🟠⚠️ Major (1) 🟠⚠️

🟠 1) scope Consider npm deprecation notice for removed package

Issue: The @inkeep/agents-manage-mcp package appears to have been published to npm (v0.48.4 with publishConfig.access: public). Deleting the package from this repo doesn't remove it from npm, but external consumers won't receive any warning that the package is deprecated.

Why: Any existing consumers of @inkeep/agents-manage-mcp who attempt to upgrade or discover the package won't know it's been superseded by @inkeep/agents-mcp. The npm registry will continue serving the old versions without deprecation warnings.

Fix: After merging, consider running:

npm deprecate @inkeep/agents-manage-mcp "This package is deprecated. Use @inkeep/agents-mcp instead."

This marks all versions as deprecated on npm and shows a warning during install.

Refs:

• npm deprecate docs

🟡 Minor (1) 🟡

🟡 1) .agents/skills/product-surface-areas/SKILL.md Summary table counts not updated after catalog removals

Issue: The summary table at lines 14-27 shows MCP Servers & Endpoints | 7 and Total | 63, but the PR removed 2 entries from the MCP catalog section (Manage MCP Server and Manage MCP Endpoint). The actual count is now 5, and the total should be 61.

Why: Inconsistent counts between the summary and catalog can cause confusion for AI agents and developers using this skill file for surface area analysis.

Fix: Update the summary table:

- | MCP Servers & Endpoints | 7 |
+ | MCP Servers & Endpoints | 5 |
...
- | **Total** | **63** |
+ | **Total** | **61** |

Refs:

• product-surface-areas/SKILL.md:19

💭 Consider (1) 💭

💭 1) create-agents-template/pnpm-lock.yaml Stale lockfile reference to removed package

Issue: The create-agents-template/pnpm-lock.yaml contains transitive dependency references to @inkeep/agents-manage-mcp@0.48.4 from published @inkeep/agents-api@0.48.4.

Why: This is expected behavior — the lockfile reflects published npm registry versions (v0.48.4 predates this removal). The reference will naturally resolve when the next version is published and the lockfile is regenerated. However, if @inkeep/agents-manage-mcp is ever unpublished from npm, the lockfile could cause resolution failures.

Fix: No immediate action required. The lockfile will update naturally on the next release cycle. Optionally, if you want to clean it now: cd create-agents-template && pnpm install --lockfile-only after publishing the next version.

🕐 Pending Recommendations (1)

• 🟠 No changeset — The changeset-bot already flagged that this PR has no changeset. If the /manage/mcp endpoint was customer-facing, consider adding one documenting the removal.

---

💡 APPROVE WITH SUGGESTIONS

Summary: This is a clean deprecation removal PR that successfully deletes the @inkeep/agents-manage-mcp package and /manage/mcp endpoint, consolidating MCP functionality into the unified @inkeep/agents-mcp package. The cleanup is thorough across build configs, skill files, and API routes. The only actionable items are: (1) updating the skill file summary counts to reflect the removed entries, (2) considering an npm deprecation notice for external consumers, and (3) deciding whether a changeset is needed for changelog purposes. The /mcp endpoint using the replacement package remains fully functional.

Discarded (3)

Location	Issue	Reason Discarded
agents-api/CHANGELOG.md	Historical references to agents-manage-mcp	Appropriate historical records that should be preserved
.agents/skills/*.md	AI artifact accuracy	Positive finding — the skill files were correctly updated
create-agents-template/pnpm-lock.yaml	Transitive dependency will cause install failures	The package remains published on npm; lockfile will resolve naturally on next release

Reviewers (3)

Reviewer	Returned	Main Findings	Consider	While You're Here	Inline Comments	Pending Recs	Discarded
pr-review-devops	3	0	1	0	0	1	1
pr-review-breaking-changes	4	1	0	0	0	1	2
pr-review-consistency	3	1	0	0	0	0	2
Total	10	2	1	0	0	1	5

Note: Changeset finding was deduplicated (raised by both devops and breaking-changes reviewers) and routed to Pending Recs since changeset-bot already flagged it.

[claude]

PR Review Summary

(0) New Issues | (2) Pending from Prior Review | Risk: Low

This is a re-review following a formatting commit. No new issues were identified — all findings from sub-reviewers duplicate issues already raised in the prior automated review.

🕐 Pending Recommendations (2)

The following issues were raised in the prior review and remain unaddressed:

• 🟠 scope — npm deprecation notice: After merging, run npm deprecate @inkeep/agents-manage-mcp "This package is deprecated. Use @inkeep/agents-mcp instead." to warn existing consumers.

• 🟡 .agents/skills/product-surface-areas/SKILL.md:19 — Summary table counts not updated: The summary shows MCP Servers & Endpoints | 7 and Total | 63, but the catalog now has 5 MCP entries. Update to | 5 | and | 61 |.

---

💡 APPROVE WITH SUGGESTIONS

Summary: This PR cleanly removes the deprecated @inkeep/agents-manage-mcp package and /manage/mcp endpoint, consolidating MCP functionality into the unified @inkeep/agents-mcp package. The cleanup is thorough across build configs, API routes, and skill documentation. A human reviewer has already approved. The only remaining items are the two pending recommendations from the prior review — the skill file count mismatch (Minor, quick fix) and the npm deprecation notice (post-merge action). Ship it! 🚀

Discarded (2)

Location	Issue	Reason Discarded
create-agents-template/pnpm-lock.yaml	Transitive reference to removed package	Expected behavior — lockfile reflects published npm versions; will resolve naturally on next release cycle
agents-api/CHANGELOG.md	Historical references to agents-manage-mcp	Appropriate historical records that should be preserved

Reviewers (3)

Reviewer	Returned	Main Findings	Consider	While You're Here	Inline Comments	Pending Recs	Discarded
pr-review-devops	2	0	0	0	0	1	1
pr-review-breaking-changes	1	0	0	0	0	1	0
pr-review-consistency	1	0	0	0	0	1	0
Total	4	0	0	0	0	2	1

Note: All 3 reviewers identified the skill file counts issue — deduplicated and routed to Pending Recs since it was already raised in the prior automated review.