Scala: wait for Metals' reported work, not a fixed 5 seconds (#1859)

Cross-file queries waited 5s after the first file was opened. On a cold Metals
that is long before it has imported the build, indexed, and — crucially —
compiled: references come from SemanticDB, which the build server writes as it
compiles, so a query made in between returns some of the references rather than
none, with nothing to mark it partial. Against a ~700-file Scala 3 build the
first find-references returned 124 of 242.

Metals already reports all of this as work-done progress; Serena did not declare
`window.workDoneProgress`, so none of it arrived. Declare it, track the tokens,
and wait for them before the first cross-file query — the same event-based shape
as TypeScript's indexing wait (#1639), whose hooks this uses.

Readiness is "nothing outstanding for a moment", not "nothing outstanding":
Metals hands off between its phases rather than overlapping them, so the token
set empties for around a second between the import ending and indexing starting,
and a plain drain returns in that gap. Measured on the same build, the first
find-references now returns all 242, taking 32s rather than 22s.

docs/02-usage/050_configuration.md

@@ -1112,6 +1112,13 @@ build below the repository root — it is the build roots, not the repository ro
 given. Serena detects them automatically; `project_roots` overrides that detection where it guesses
 wrong, and `project_root_scan_depth` bounds how far it looks.
 
+Metals reports its build import, indexing and compilation as LSP work-done progress, and Serena waits
+for all of it before the first cross-file query of a session. This matters most for references, which
+Metals serves from SemanticDB — a file the build server only writes once it has compiled the sources,
+well after indexing ends — so a query made too early returns a fraction of the true result with
+nothing to say it is partial. The wait is bounded by `indexing_timeout`, after which the query
+proceeds against whatever Metals has so far and a warning is logged.
+
 Supported settings:
 
 | Setting | Default | Description |
@@ -1123,6 +1130,9 @@ Supported settings:
 | `auto_import_build` | `true` | Answer Metals' build-import prompts affirmatively, which lets it run the project's build tool (e.g. `sbt bloopInstall`). Set to `false` to leave the build un-imported; Metals then has no build server, and every cross-file query is served by the fallback presentation compiler. |
 | `project_roots` | auto-detected | The build roots to serve, as paths relative to the repository root. A path that does not exist is skipped with a warning; if none of them exists, the build roots are detected instead. |
 | `project_root_scan_depth` | `3` | How many directory levels below the repository root the detection searches. Applies whenever the roots are detected — that is, when `project_roots` is unset, or when it names nothing that exists. |
+| `indexing_timeout` | `180` | How long to wait, in seconds, for Metals to finish importing, indexing and compiling before the first cross-file query. On expiry the query proceeds and a warning names what was still outstanding. |
+| `indexing_start_grace` | `15` | How long to wait, in seconds, for Metals to report any work at all. A server that reports none within this window is taken to have nothing to do. |
+| `indexing_quiet_period` | `3` | How long, in seconds, Metals must report nothing for its work to count as finished. Metals hands off between its phases rather than overlapping them, so it reports nothing for a moment in between; a shorter period risks mistaking that gap for completion. |
 
 #### SCSS / Sass / CSS