Changing permissions of an input file does not cause its actions to rerun

This is not affecting me personally and I consider it pretty low priority — in fact I'm not sure if you would consider it a bug — but I'm filing it in case it's something you want to address.

### Description of the problem / feature request / question:

Changing the permissions of an input file (e.g. with chmod) do not cause any actions that have that file as an input to rerun. Seems like this might be a bug, although the only scenarios I've been able to come up with are somewhat contrived, such as the example below.

### If possible, provide a minimal example to reproduce the problem:

`BUILD` file:

```
genrule(
name = "main",
srcs = ["main.in"],
outs = ["main.out"],
cmd = "if [[ -x $(SRCS) ]]; then echo $(SRCS) is executable > $@; else echo $(SRCS) is not executable > $@; fi"
)
```

Then, `touch main.in` and then `bazel build :main`. As expected, bazel-genfiles/main.out will say: `main.in is not executable`

Then, `chmod +x main.in` and `bazel build -s :main`. Nothing rebuilds, and bazel-genfiles/main.out has not changed.

### Environment info
* Operating System: OSX and Linux

* Bazel version (output of `bazel info release`): 0.5.2

Start with the minimal BUILD file and reproduce the sequence using main.in: run bazel build :main, change its permissions with chmod, then run bazel build -s :main. Done means the action reruns after the permission change and main.out reflects whether main.in is executable on OSX and Linux.

Written by the indexing model from the issue text.