copyDirectory fails on read-only files.

[DanGrayson]

Since the Style package has a Makefile created from its Makefile.in in its auxiliary files directory, "installPackage" was failing on it, because "copyDirectory" has a problem.

Perhaps add an option to copyDirectory so it forcibly replaces read-only files.

Macaulay2, version 1.9
with packages: ConwayPolynomials, Elimination, IntegralClosure, LLLBases, PrimaryDecomposition, ReesAlgebra, TangentCone

i1 : copyDirectory("a", "b")

i2 : copyDirectory("a", "b")
stdio:2:1:(3): error: opening output file "b/foo" failed: Permission denied

i3 : run "ls -l a"
total 0
-r--r--r-- 1 dan dan 0 May  5 14:53 foo

o3 = 0

i4 : run "ls -l b"
total 0
-r--r--r-- 1 dan dan 0 May  5 14:53 foo

o4 = 0