fix(settings): stop ALTER SETTINGS dropping configuration data and silently ignoring invalid values

[ako]

Fixes two upstream issues in the project-settings write path. Both are in ALTER SETTINGS, but they are independent bugs and land as separate commits.

• ALTER SETTINGS (any command) silently corrupts every constant override in the project, and drops CustomSettings/Tracing, on write mendixlabs/mxcli#801 — ALTER SETTINGS (any command) silently corrupts every constant override in the project, and drops CustomSettings/Tracing, on write
• ALTER SETTINGS CONFIGURATION silently ignores invalid Integer-typed values while reporting success mendixlabs/mxcli#805 — ALTER SETTINGS CONFIGURATION silently ignores invalid Integer-typed values while reporting success

Issue numbers above refer to mendixlabs/mxcli, not this fork.

0b4feb7 — overlay server configurations instead of rebuilding them (mendixlabs#801)

serverConfigurationToBSON re-serialized each Settings$ServerConfiguration from model.ServerConfiguration, which carries only the fields mxcli models. Everything else in the stored document was therefore deleted on write. The reported symptoms plus two more found while reproducing:

What was lost	Reported?
CustomSettings emptied	yes
Tracing nulled	yes
constant overrides rewritten with a flat Value instead of the nested SharedOrPrivateValue the platform reads	yes
OpenAdminPort / OpenHttpPort reset to false — never populated on read, so the model always held the zero value	no
Configurations / ConstantValues / CustomSettings version markers downgraded 3 → 2	no

The configurations are now overlaid onto the raw document they were read from — the ADR-0005 guard-don't-drop form the surrounding settings parts already used. Only fields the read path populates get written, each list keeps its stored marker, and a constant override is updated in whichever slot it already occupies (nested if nested, flat if flat, per the issue's "maintain original storage shapes"). A brand-new override has no stored shape to preserve and is written nested. CREATE CONFIGURATION derives its shape from a sibling, empties the per-configuration collections, and mints a fresh $ID.

Two things beyond the issue as filed:

1. The legacy engine had the identical bug (sdk/mpr/writer_settings.go, same logic in bson.D form). --engine legacy is a documented fallback, so leaving it would keep the same data loss reachable. Rather than duplicate the fix, the overlay is extracted into mdl/settingsoverlay and shared by both engines, so they cannot drift apart again.
2. A write with empty RawParts would have replaced every settings part with an empty array, resetting the whole Project Settings dialog. readSettingsRawParts returns nil on any read error, so this was reachable. Both engines now refuse the write instead.

Known limitation, stated in the commit message: a project whose overrides were already flattened by an earlier mxcli run keeps the flat shape, because the overlay preserves what is stored rather than converting it. Those overrides need re-entering in Studio Pro once. Auto-upgrading flat → nested was deliberately left out: there is no ground truth on whether Mendix 9 legitimately stores flat, and no fixture in the repo has a Studio Pro-authored constant override to check against. With a real ConstantValue from a 9.x and an 11.x project the repair could be made unconditional.

4deca96 — reject invalid typed values instead of ignoring them (mendixlabs#805)

All seven strconv.Atoi sites discarded the parse error (if v, err := strconv.Atoi(valStr); err == nil), so an unparseable value skipped the assignment while the handler still printed its success line: BcryptCost, DefaultTaskParallelism, WorkflowEngineParallelism, and HttpPortNumber / ServerPortNumber on both ALTER SETTINGS CONFIGURATION and CREATE CONFIGURATION.

The boolean settings had the same hole in a different form: AllowUserMultipleSessions = valStr == "true" mapped every other spelling — a typo, or a plausible 'yes' — to false and reported success. The issue's "other typed configuration settings exhibiting similar behavior" covers it, so it is fixed here too.

mxcli check also passed the invalid script cleanly, which is the same silent acceptance one layer up. Added MDL-SET01 (integers) and MDL-SET02 (booleans), wired into mxcli check and the LSP, so a typo surfaces before the project is opened for writing. That is also what makes the .fail.mdl regression fixture meaningful — make check-mdl only runs mxcli check, so an executor-only fix would have had no CI gate. TestTypedSettingsKeys_MatchExecutor guards the new check-time table against drifting from the executor's assignment switch.

Out of scope, stated in the commit message: range validation. A port of 0 or 999999, or a negative BcryptCost, still parses as an integer and is accepted, as before.

b87e1b9 — make make lint pass under TypeScript 6

Unrelated to either issue, included because make lint failed on a clean checkout of main with 43 TypeScript errors and CLAUDE.md requires it to pass. bun install floats typescript to ^6.0.2, which no longer auto-includes every @types/* package on disk — they must be listed in types. Adding "types": ["node", "vscode"] left one genuine error: vscode-languageclient 10 wants a LogOutputChannel, so the output channel is created with { log: true }. CI only runs make lint-go, which is why this went unnoticed.

Drop this commit if you would rather keep the upstream PR to the two issues — it is self-contained and touches only vscode-mdl/.

Testing

make build, make test, make lint and make check-mdl all pass.

New coverage:

• mdl/settingsoverlay/settingsoverlay_test.go — unit tests for the overlay: unknown-key preservation, marker preservation, the three constant-value shape paths, sibling-derived new configurations.
• mdl/backend/modelsdk/settings_write_configuration_test.go — round-trip against a seeded fixture (the fixture project has no overrides, custom settings or Tracing, so they are seeded first). Verified this test reproduces all six facets of ALTER SETTINGS (any command) silently corrupts every constant override in the project, and drops CustomSettings/Tracing, on write mendixlabs/mxcli#801 against the pre-fix code before the fix went in.
• mdl/executor/cmd_settings_validation_test.go — every rejection path asserts no write was attempted and no success line printed, plus the accept-valid cases (quoted number, numeric literal, padded, both booleans) so the fix does not over-reject.
• mdl-examples/bug-tests/801-alter-settings-preserves-configuration.mdl — repro with Studio Pro verification steps (needs a project, so it is a syntax-pass fixture only).
• mdl-examples/bug-tests/805-alter-settings-typed-values.fail.mdl — negative fixture, gated by make check-mdl.

Docs: two rows appended to the .claude/skills/fix-issue.md symptom table, MDL-SET01 / MDL-SET02 registered in docs-site/src/tools/builtin-rules.md, and a note on typed values in the project-settings skill.

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