* Generalize ChiselAnnotation

This allows us to delay creation of Annotations till elaboration is
complete. Also update all annotation-related code.

* Add RunFirrtlTransform

Use a Chisel-specific RunFirrtlTransform API to preserve behavior of old
ChiselAnnotation (now called ChiselLegacyAnnotation)

* Use unique test directories in ChiselRunners.compile

Add companion objects to macro classes

Workaround for unconditional invalidation of macro classes in
incremental recompilation

* Remove checkboxes from issue/pr templates.

* Compact template text and try to make meta information comments.

* Respond to comments - remove bullet point usage.

Revert "Aggregate coverage - discover a working combination of aggregate usage to enable coverage of subprojects. (#782)" (#786)

This is still broken - it publishes multiple jars.
This reverts commit e08da912.

Aggregate coverage - discover a working combination of aggregate usage to enable coverage of subprojects. (#782)

* Generate aggregate coverage but publish a single Jar

* Reduce the aggressive dis-aggregation as it breaks super project aggregation.

* trying to get aggregate coverage working again ...

* Use the right incantation to enable aggregation for only the coverageReport task.

It appears #754 breaks more code than I thought, so this makes it a soft error (with a runtime deprecation warning - to get people to fix their stuff before we break it for real) for now.

This additionally changes the autoclonetype errors to be more deterministic (reporting class names instead of object names) in the most common cases, to allow the deprecations manager to deduplicate warnings.

Changes the API such that IO(...) clones. All Bundles will need to be clone-able, but auto clone type is expected to handle most cases.

* Better support for autoclonetype of nested Bundles

* Move bundleStack to dynamicContext

* prefer $outer if available, make guesses distinct

* Catch IllegalAccessException in autoclonetype
In strange circumstances this type of exception can occur when accessing $outer

BuildInfo.BuildTime appears to cause sbt to always recompile BuildInfo to get
the latest time, which causes a recompile on any package that depends on
chisel3. This is quite painful for doing development on any Chisel projects.
BuildTime doesn't actually appear to be in use, and removing it fixes the
unnecessary recompilation issue.

Add runtime warnings for use of deprecated Chisel methods. This is done using a macro that takes the message from a `@deprecated` annotation, and adds a call to `Builder.deprecated`.

Reasoning is that by default, Scala doesn't print all deprecations, and that it's somewhat tricky to notice them - yet some support questions revolve around the use of deprecated and terribad API. This now prints warnings for uses of deprecated functions at runtime, and aggregates them by error and line to avoid spam. Also included is convenient information on enabling scalac deprecations.

This also changes how line numbers for Chisel's error facility is determined, using prefix string comparison of the stack trace element classnames, instead of checking if the class is a subtype of UserModule. The previous one (specifically, calls to Class.forName) seems to interact badly with reflection-based cloneType when called at scale. This should also give more accurate reporting of errors that are in user code but outside of a UserModule.

It turns out that `@deprecated` on macro functions don't do anything, so this changes the tags to the functions that the macros point to, which seems to work properly. It also turns out that there's a bunch of uses of deprecated functions in chiselTests which needs to be fixed.

Not all `@deprecated` functions are also annotated with `@chiselRuntimeDeprecation`, because they're still used in Chisel internals, and we can't track whether they're called by the user or by Chisel and it will give a misleading error. These are a small amount of functions.

Auto clone type 🦆

Also change Data.outerModule to Bundle._outerInst since it is only used
in autoclonetype. _outerInst is also Option[Object] instead of
Option[BaseModule] because the outer object could also be a Bundle.

Fixes #748

Fixes #746
Also add test for https://github.com/freechipsproject/firrtl/issues/705

Prevents DontCare from affecting type inference
Fixes #728

Fixes #708

Make InvalidateAPI emit to a test directory
Add *.swp and test_run_dir to .gitignore

Fixes #482