feat: Add repository (project) token support OD-489

[alerizzo]

Summary

• Adds --repository-token <token> (and CODACY_PROJECT_TOKEN) to every command, sent as the project-token header. CI no longer needs a personal account token that reaches every org and repo the user can see.
• Precedence matches analysis-cli#104 exactly: --repository-token > CODACY_PROJECT_TOKEN > CODACY_API_TOKEN > stored login. An explicit flag wins outright, so a scoped run is never silently widened. Auth is now a RemoteAuth discriminated union carrying the token kind and its source, so refusals can name where the token came from.
• Codacy honours repository tokens on only 13 operations, so commands outside that set refuse before sending anything — and before the git auto-detection line — rather than surfacing a bare Unauthorized. Verified: refusals return in ~115 ms against a black-holed base URL; supported commands still reach the network.
• codacy repository skips its two non-whitelisted calls (listRepositoryPullRequests, listCoverageReports) and marks them in JSON as "unavailable": ["pullRequests"], keeping pullRequests an iterable [] so existing jq consumers don't break. Under an account token the payload is byte-identical to before.
• tool, patterns, and pattern needed no logic changes — every endpoint they touch was already whitelisted.

Also fixes two pre-existing bugs found along the way:

• codacy repository lost the entire dashboard when the pull-request lookup failed (its three sibling calls were already .catch()-guarded).
• codacy login --token <repo-token> reported "Invalid API token. Check that it is correct and not expired" — wrong advice for a token that's fine but the wrong kind, since /user rejects repository tokens by design.

New docs: SPECS/repository-tokens.md (whitelist + per-command support matrix, re-verify on every npm run update-api) and SPECS/missing-endpoints.md (ranked gaps, as candidate follow-up tasks — listRepositoryPullRequests is the standout, being the only reason repository degrades at all).

Closes OD-489.

Test plan

• npm test — 606 pass (40 new), including 11 refusal tests asserting the guarded service was never called
• npm run build && npx tsc --noEmit
• Header on the wire (verified against a local listener): CODACY_PROJECT_TOKEN → project-token; CODACY_API_TOKEN → api-token; never both; no empty api-token on repository-token runs
• Fail-fast: with CODACY_API_BASE_URL=http://127.0.0.1:9 and only a repository token, each of info, repositories, ls, directories, pull-request(s), issue, findings, finding, repo --add/--remove/--follow/--unfollow/--link-standard/--unlink-standard, issues --ignore/--ignored exits 1 in well under a second
• Account-token regression: codacy repo -o json unchanged (no unavailable key, real pullRequests); info/ls/pull-requests/issues --ignored still work
• End-to-end: run the configure-codacy-cloud skill against a real repo with only CODACY_PROJECT_TOKEN set — the acceptance criterion for OD-489. Full manual script in SPECS/repository-tokens.md.

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[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

View in Codacy

🟢 Metrics 34 complexity · 210 duplication

Metric	Results
Complexity	34
Duplication	210

View in Codacy

AI Reviewer: first review requested successfully. AI can make mistakes. Always validate suggestions.

_{TIP This summary will be updated as you push new changes.}

[codacy-production]

Pull Request Overview

The repository token support implementation is functionally complete and correctly adheres to the specified precedence model (flag > env > stored) and header usage (project-token).

However, the PR is currently 'not up to standards' according to Codacy. Key concerns include:

• Complexity: src/commands/login.ts has grown too complex due to identity resolution and error handling. src/commands/repository-token-refusals.test.ts (complexity: 22) and src/commands/repository.ts (complexity: 10) also show high complexity scores.
• Cloning: There is a substantial delta in code clones (+206), which should be investigated to ensure the test suites are not duplicating logic unnecessarily.
• File Length: src/commands/pattern.test.ts has exceeded the 500-line threshold.

All functional test scenarios, including fail-fast guards and the degraded 'repository' dashboard, are reported as found.

About this PR

• The PR introduces 206 new clones and increases complexity in core command files (notably login.ts and repository.ts). This systemic increase suggests that the logic for handling token-based branching and fail-fast guards may need more abstract, reusable patterns rather than inline condition checks.

1 comment outside of the diff

src/commands/pattern.test.ts

_{line 1 ⚪ LOW RISK}
Consider splitting this test file into smaller, focused modules (e.g., pattern-info.test.ts for read operations and pattern-config.test.ts for modification logic) to stay within file length guidelines.

Test suggestions

• Token precedence order (flag > project env > api env > stored login)
• Header selection: account token uses 'api-token', repo token uses 'project-token'
• Fail-fast guards: verify account-only commands (e.g., info, findings) exit early with descriptive messages
• Mixed-mode 'repository' dashboard: skips PR/coverage calls but renders metrics under a repo token
• Mixed-mode 'repository' JSON: verify 'unavailable' field and presence of empty pullRequests array
• Import guard: 'tools --import --force' refusal when organization-level unlinking is required
• Login/Logout warnings: verify warnings are issued only for explicit flag usage, not ambient env vars
• Regression: Account token continues to see full dashboard and PR listings

_{TIP Improve review quality by adding custom instructions
TIP How was this review? Give us feedback}

[codacy-production]

_{🟡 MEDIUM RISK}

Document a clear exception or escalation process alongside this absolute rule. Include criteria for when an exception might apply and who can authorize it.

See Issue in Codacy

[alerizzo]

Fair — the rule is absolute but the exception was left implicit. Added two sub-bullets: commands whose endpoints are all whitelisted need no guard at all (tool, patterns, pattern are the live examples), and when an operation's scope is genuinely unclear the escalation is to confirm against the API owners and record it in SPECS/repository-tokens.md rather than guess a guard.

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[codacy-production]

_{🟡 MEDIUM RISK}

The action handler logic is doing too much. Extract the user identity resolution and the detailed 401/403 error handling into a dedicated helper function (e.g., resolveAndValidateUser) to improve maintainability and reduce cyclomatic complexity.

Try running the following prompt in your IDE agent:

Refactor the .action handler in src/commands/login.ts to extract the authentication validation and error handling (lines 78-103) into a separate helper function.

See Issue in Codacy
See Issue in Codacy

[alerizzo]

Good catch — fixed. Extracted resolveAndValidateUser() (validation + the 401/403 branches) and acquireToken() (flag vs. interactive prompt). The action handler is now CCN 2 / 18 NLOC, down from 9 / 61; both helpers are well under the limits too.

Worth noting the CCN 9 was pre-existing on main — it surfaced here only because this PR touched that function — so this is a real cleanup rather than a regression being papered over.

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[codacy-production]

_{⚪ LOW RISK}

Suggestion: Split this into separate bullet points to ensure both actions are clearly visible to the reader.

Suggested change

	- The whitelist is hardcoded in these guards. **Re-verify it after every `npm run update-api`.**
	- The whitelist is hardcoded in these guards.
	- **Re-verify it after every `npm run update-api`.**

See Issue in Codacy

[alerizzo]

Agreed — split into two bullets.

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[codacy-production]

_{⚪ LOW RISK}

Suggestion: Split this instruction into separate points for account tokens and repository tokens to improve clarity.

Suggested change

	- An **account token** (`api-token` header) reaches everything its owner can see. A **repository token** (`project-token` header) is scoped to one repository and is accepted only on a fixed whitelist of 13 operations; everywhere else Codacy rejects it as if no token had been sent.
	- An **account token** (`api-token` header) reaches everything its owner can see.
	- A **repository token** (`project-token` header) is scoped to one repository and is accepted only on a fixed whitelist of 13 operations; everywhere else Codacy rejects it as if no token had been sent.

See Issue in Codacy

[alerizzo]

Agreed — split into one bullet per token kind, as suggested.

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[alerizzo]

Review round 1 — resolved

All 4 inline comments addressed (replies inline). Codacy's new-issue count went 5 → 0:

Issue	Resolution
login.ts CCN 9 / 61 NLOC	Fixed — extracted acquireToken() + resolveAndValidateUser(); handler now CCN 2 / 18 NLOC
AGENTS.md sentence-complexity	Fixed — split into one bullet per token kind
AGENTS.md compound-instruction	Fixed — split into separate bullets
AGENTS.md escape-hatch-missing	Fixed — documented the exception (all-whitelisted commands need no guard) and the escalation path
AGENTS.md compound-instruction (2nd)	Dismissed — false positive, see below
pattern.test.ts file-nloc 515	Dismissed — long test files are deliberate here; fixtures are written out in full so each test reads standalone
AGENTS.md outdated-cross-reference	Dismissed — false positive; SPECS/repository-tokens.md is added in this same PR

On the dismissed compound-instruction: it flags - **Re-verify the whitelist after every npm run update-api.** — a single action. The rule seems to count actions across the parent bullet's nested children rather than the flagged bullet, so splitting the block twice only walked the flag further down it. It also pulls against clarity_escape-hatch-missing on the same block, which asked for more detail. Contorting the doc further would make it worse to read, so it's marked false-positive with that reasoning.

Also added .codacy/instructions/review.md capturing the project-specific context behind this round's false positives, so future reviews don't repeat them (long test files are intentional; Lizard's TS parser merges adjacent function spans, inflating reported complexity; the token whitelist is hardcoded on purpose because it mirrors a server-side allowlist the client can't query). .codacy/ was gitignored wholesale, so the rule is narrowed to .codacy/* — all local CLI state stays ignored.

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[alerizzo]

Adversarial review round (Sonnet 5 × 3 + /code-review)

Ran four independent review passes. One real bug surfaced, plus a doc/behaviour mismatch and some test-strength gaps. All fixed in 489c132.

🔴 Empty --repository-token silently widened scope to an account token.

--repository-token "$CODACY_PROJECT_TOKEN" with the secret unset or misspelled passed an empty string, which resolved as "no flag" and fell through to an ambient CODACY_API_TOKEN or a stored login. A CI job asking for a repository-scoped run authenticated with a full account token — the exact widening the precedence rule promises cannot happen. Confirmed against a local listener, before and after:

before:  --repository-token ""  →  sent: api-token=SECRET-ACCOUNT-TOKEN
after:   --repository-token ""  →  Error: --repository-token was given an empty value…

An explicitly-passed empty flag is now refused. Empty env vars keep meaning "unset" (the asymmetry is deliberate — the test config depends on it). Flag and env values are trimmed, so whitespace-only tokens get the CLI's own error instead of a server 401. Controls re-verified on the wire: real token → project-token, padded → trimmed, no flag → api-token, whitespace-only env → falls through.

🟠 Coverage was skipped silently while the docs claimed it was marked. Skipping listCoverageReports forces expectsCoverage false, which suppresses the "waiting for / missing coverage reports" state — so a repo configured for coverage but missing reports rendered identically to a healthy one, with nothing in JSON to say otherwise. unavailable now lists coverageReports alongside pullRequests; README and SPECS/repository-tokens.md corrected.

🟡 Two dashboard tests gave false confidence. Mutation testing (revert the skip, re-run) proved they asserted only on the token-kind branch and passed with the optimization removed. They now assert the calls were genuinely never made. Also added the untested CODACY_PROJECT_TOKEN vs stored-credentials precedence case, the account-token JSON failure path, and moved CODACY_PROJECT_TOKEN cleanup into afterEach so a failing assertion can't leak the highest-precedence token into later tests.

Clean under adversarial scrutiny: the 13-operation whitelist (every "supported" path walked against the generated services — no missed call), guard ordering, the prsUnavailable write inside Promise.all (no race — Promise.all can't resolve until the .catch handler completes), pickDeep genuinely omitting unavailable, and optsWithGlobals behaviour verified against the installed commander source rather than assumed.

610 tests pass (+4).

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