feat(@deepnote/cli): support linting integrations env yaml file directly - #337

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@packages/cli/src/commands/lint.test.ts`:
- Around line 774-793: The test for createLintAction in lint.test.ts only
asserts integrationsFile.issues and exit behavior and misses verifying the
top-level JSON contract on failures; update the failing-case tests (e.g., the
'outputs JSON with issues for an invalid integrations yaml file' case that calls
action(intFile, { output: 'json' })) to also assert parsed.success is false and
parsed.issueCount.errors > 0 and parsed.issueCount.total > 0 (and add a similar
assertion in one notebook+integrations failure test) so configuration failures
cannot serialize as success: true or zero issue counts; locate and modify the
tests that call createLintAction/action and parse JSON output to include these
additional assertions.
- Around line 1242-1257: The test currently assumes a missing user-specified
integrations file silently yields an empty config; instead, update the CLI's
lint handling so that when the integrationsFile option is provided but the file
does not exist you surface an error and exit with invalid-usage semantics;
locate the lint option parsing / handler (createLintAction and the lint command
logic in packages/cli/src/commands/lint.ts) and change the branch that reads
integrationsFile to validate existence and throw or call the existing error/exit
path (same style as the direct YAML path handling around the existing error
block) rather than falling back to an empty integrations result.

In `@packages/cli/src/commands/lint.ts`:
- Around line 112-120: The returned lint status currently spreads the result of
lintFile() and embeds a hardcoded integrationsFile object from
lintIntegrationsFile() which sets zero issue counts, so invalid integrations
produce inconsistent success/issueCount; update
lintIntegrationsFile(integrationsFilePath, parsedIntegrations) to compute and
return true issue counts (issueCount.total and per-category counts) and a
success boolean based on parsedIntegrations.issues and
parsedIntegrations.integrations parsing results, and then merge those counts
into the top-level lint object returned by the function that builds the final
result (the block returning { path: absolutePath, ...lint, integrationsFile: {
... } }) so that overall issueCount and success reflect both lintFile() and
lintIntegrationsFile() outcomes. Ensure you reference lintFile(),
lintIntegrationsFile(), parsedIntegrations and the returned integrationsFile
fields when making the change.
- Around line 82-103: The lint command currently mutates process.env by calling
dotenv.config(...) and injecting envVars from
getEnvironmentVariablesForIntegrations(parsedIntegrations.integrations, ...)
without restoring originals, causing subsequent lint runs in the same process to
see stale/overwritten values; fix by saving the original environment state (for
each env var you will set and the result of dotenv.config), apply the dotenv and
injected envVars only for the duration of the lint run (the logic around
parseIntegrationsFile / getEnvironmentVariablesForIntegrations and subsequent
checks), and restore process.env to its prior values after the lint completes or
on error (ensure restoration covers both newly added vars and overwritten values
so caller-provided envs are preserved); use the function/variable names
parseIntegrationsFile, getEnvironmentVariablesForIntegrations, dotenv.config,
and the envVars loop to locate where to capture and later restore the original
environment.

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Outside diff comments:
In `@packages/cli/src/commands/lint.ts`:
- Around line 165-177: The returned object from lintIntegrationsFile currently
sets issueCount to zeros and issues to an empty array despite parsedIntegrations
containing real issues; update the return to compute issueCount from
parsedIntegrations.issues (set errors/warnings/total appropriately—e.g. count by
severity and sum for total), set issues to parsedIntegrations.issues, and keep
success as !hasErrors; reference lintIntegrationsFile, parsedIntegrations,
issueCount, and integrationsFile in your changes.
- Around line 126-135: The returned lint result currently spreads lint and sets
success using parsedIntegrations.issues but leaves issueCount unchanged, so
issueCount.errors remains zero when config errors exist; update the returned
object to compute a combined issueCount by merging lint.issueCount with
parsedIntegrations.issues (e.g., increment errors and total counts or otherwise
aggregate parsedIntegrations.issues.length into lint.issueCount.errors and
total) before returning, referencing the variables absolutePath, lint,
parsedIntegrations, success, and integrationsFile so consumers relying on
issueCount.errors see config-related errors.

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@packages/cli/src/commands/lint.test.ts`:
- Line 3: Tests produce OS-dependent snapshots because file paths returned by
join/relative/resolve use backslashes on Windows; update the snapshot helper
used in lint.test.ts (and any assertions around the calls to relative() / join()
/ resolve at the lines referenced) to normalize path separators before
snapshotting by converting platform separators to '/' (e.g., replace all
backslashes with '/'), or use path.posix equivalents so snapshots are stable
across OSes; ensure the normalization runs on the strings produced by relative()
/ join() / resolve prior to creating the snapshot.

---

Outside diff comments:
In `@packages/cli/src/commands/lint.test.ts`:
- Around line 934-949: The test suite is leaking environment variables set by
lintFile (from packages/cli/src/commands/lint.ts), so capture process.env in
beforeEach (e.g., const originalEnv = { ...process.env }) and restore it in
afterEach (assign process.env = originalEnv) in addition to calling
vi.unstubAllEnvs(); update the existing beforeEach/afterEach that set up
program, console spies, exitSpy and call resetOutputConfig() to include the env
snapshot/restore to ensure SQL_* vars injected by lintFile are cleared between
tests.
- Around line 661-672: The multiline YAML fixtures written with writeFile (e.g.,
the call that writes to intFile in packages/cli/src/commands/lint.test.ts) are
raw indented template strings; wrap them with ts-dedent to normalize
indentation. Import dedent from "ts-dedent" if not already, and replace the
literal template strings passed to writeFile with dedent(`...`) so the fixture
content is stable; apply the same change to the other similar fixtures mentioned
(lines around 808-812, 987-996, 1336-1345).